diff --git a/CHANGELOG.md b/CHANGELOG.md index 7a2f87f2..7cecf923 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -127,16 +127,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Module updates -| Tool | Old version | New version | -| ---------- | ----------- | ----------- | -| fqcrs | 0.1.0 | -| severus | | 1.1 | -| longphase  |   | 1.7.3   | -| genmod | 3.8.2 | 3.9 | -| WhatsHap | 2.2 | 2.3 | -| SVDB | | 2.8.1 | -| hifiasm | 0.19.8 | 0.20.0 | -| HiFiCNV | 0.1.7 | 1.0.0 | +| Tool | Old version | New version | +| -------------- | ----------- | ----------- | +| fqcrs | 0.1.0 | +| severus | | 1.1 | +| longphase  |   | 1.7.3   | +| genmod | 3.8.2 | 3.9 | +| WhatsHap | 2.2 | 2.3 | +| SVDB | | 2.8.1 | +| hifiasm | 0.19.8 | 0.20.0 | +| HiFiCNV | 0.1.7 | 1.0.0 | +| samtools/faidx | 1.2 | 1.21 | +| samtools/index | 1.2 | 1.21 | +| samtools/merge | 1.2 | 1.21 | +| stranger | 0.9.1 | 0.9.2 | +| multiqc | 1.21 | 1.25.1 | > [!NOTE] > Version has been updated if both old and new version information is present. diff --git a/conf/modules/short_variant_calling.config b/conf/modules/short_variant_calling.config index c53793c5..1975d044 100644 --- a/conf/modules/short_variant_calling.config +++ b/conf/modules/short_variant_calling.config @@ -34,7 +34,7 @@ process { } - withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT' { + withName: '.*:SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' { ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } ext.args = { [ "--sample_name=${meta.id}", diff --git a/modules.json b/modules.json index 4195dd68..47a9ac33 100644 --- a/modules.json +++ b/modules.json @@ -7,62 +7,63 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "682f789f93070bd047868300dd018faf3d434e7c", - "installed_by": ["modules"] + "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", + "installed_by": ["modules"], + "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", - "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/pluginsplit": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/query": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/stats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "cadd": { @@ -73,12 +74,12 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, - "deepvariant": { + "deepvariant/rundeepvariant": { "branch": "master", - "git_sha": "a7e8b8afd4fa82f20d745fa778bfdbf39c1f7efb", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "deepvariant/vcfstatsreport": { @@ -94,12 +95,12 @@ }, "fastqc": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "97321eded31a12598837a476d3615300af413bb7", "installed_by": ["modules"] }, "genmod/annotate": { @@ -124,18 +125,18 @@ }, "gfastats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "glnexus": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8", "installed_by": ["modules"], "patch": "modules/nf-core/glnexus/glnexus.diff" }, "gunzip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "hifiasm": { @@ -155,122 +156,127 @@ }, "minimap2/align": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "minimap2/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "modkit/pileup": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] }, "paraphase": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/fastq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/import": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "e9bc33485e420b51cfbed3cf63ac7463cd5739d3", - "installed_by": ["modules"] + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "installed_by": ["modules"], + "patch": "modules/nf-core/samtools/merge/samtools-merge.diff" }, "samtools/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", + "installed_by": ["modules"], + "patch": "modules/nf-core/samtools/sort/samtools-sort.diff" }, "samtools/view": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "severus": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "8a36181859504560ef333c299f6773c7b99a801f", "installed_by": ["modules"] }, "sniffles": { "branch": "master", - "git_sha": "b50aa17b1b604c7b3cfe58a2472d1e7b990ae8bf", - "installed_by": ["modules"] + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"], + "patch": "modules/nf-core/sniffles/sniffles.diff" }, "somalier/extract": { "branch": "master", - "git_sha": "f62e4cf5f0ae77dad62027ba2a9f475192f5b123", - "installed_by": ["modules"] + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"], + "patch": "modules/nf-core/somalier/extract/somalier-extract.diff" }, "somalier/relate": { "branch": "master", - "git_sha": "d8ba32c6b54a01f8efa7b51a1f3978f003f8873b", - "installed_by": ["modules"] + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"], + "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "splitubam": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "stranger": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "26cdbf29e76695c7fd85e42e0015c7e96f979fe9", "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", - "git_sha": "4ac2ef5c1ceba6bb28a73033802643093fe923b3", + "git_sha": "a8ad84b7ee0cda0b001490e95d9ed277e687e368", "installed_by": ["modules"] }, "svdb/query": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "untar": { @@ -285,17 +291,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/local/create_pedigree_file/tests/main.nf.test.snap b/modules/local/create_pedigree_file/tests/main.nf.test.snap index 9cc396b3..38ecf6ba 100644 --- a/modules/local/create_pedigree_file/tests/main.nf.test.snap +++ b/modules/local/create_pedigree_file/tests/main.nf.test.snap @@ -6,14 +6,14 @@ "family\tHG002.Revio\t0\t0\t0\t2" ], [ - "versions.yml:md5,c0d2b2d33f1c465351d65e149ae88f0c" + "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T10:24:34.60478278" + "timestamp": "2024-11-04T16:16:12.293913485" }, "create_pedigree_file - multiple samples": { "content": [ @@ -25,13 +25,13 @@ "FAM2\tHG002_Revio_AB\t0\t0\t0\t1" ], [ - "versions.yml:md5,c0d2b2d33f1c465351d65e149ae88f0c" + "versions.yml:md5,fb643cd2fc69cab285a7f0061ad223d8" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T10:40:54.71628575" + "timestamp": "2024-11-04T16:16:19.916570689" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff index 391089ff..8d3f5541 100644 --- a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -1,33 +1,17 @@ Changes in module 'nf-core/bcftools/annotate' ---- modules/nf-core/bcftools/annotate/meta.yml -+++ modules/nf-core/bcftools/annotate/meta.yml -@@ -34,6 +34,9 @@ - - header_lines: - type: file - description: Contains lines to append to the output VCF header -+ - rename_chrs: -+ type: file -+ description: Contains new and old chromosome names - output: - - meta: - type: map - +'modules/nf-core/bcftools/annotate/meta.yml' is unchanged +Changes in 'bcftools/annotate/main.nf': --- modules/nf-core/bcftools/annotate/main.nf +++ modules/nf-core/bcftools/annotate/main.nf -@@ -8,10 +8,9 @@ - 'biocontainers/bcftools:1.20--h8b25389_0' }" - +@@ -10,6 +10,7 @@ input: -- tuple val(meta), path(input), path(index) -- path(annotations) -- path(annotations_index) -+ tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) + tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) path(header_lines) + path(rename_chrs) output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf -@@ -27,6 +26,7 @@ +@@ -25,6 +26,7 @@ def prefix = task.ext.prefix ?: "${meta.id}" def header_file = header_lines ? "--header-lines ${header_lines}" : '' def annotations_file = annotations ? "--annotations ${annotations}" : '' @@ -35,13 +19,22 @@ Changes in module 'nf-core/bcftools/annotate' def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : -@@ -43,6 +43,7 @@ +@@ -40,6 +42,7 @@ + annotate \\ $args \\ $annotations_file \\ - $header_file \\ + $rename_chrs_file \\ + $header_file \\ --output ${prefix}.${extension} \\ --threads $task.cpus \\ - $input +'modules/nf-core/bcftools/annotate/environment.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged ************************************************************ diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 3d4e3379..5c00b116 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 06eb6d34..b6b73309 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -42,8 +42,8 @@ process BCFTOOLS_ANNOTATE { annotate \\ $args \\ $annotations_file \\ - $header_file \\ $rename_chrs_file \\ + $header_file \\ --output ${prefix}.${extension} \\ --threads $task.cpus \\ $input @@ -62,12 +62,12 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" - def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" """ ${create_cmd} ${prefix}.${extension} diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 78f806a4..5bfccd2b 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -13,52 +13,64 @@ tools: documentation: https://samtools.github.io/bcftools/bcftools.html#annotate doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Query VCF or BCF file, can be either uncompressed or compressed - - index: - type: file - description: Index of the query VCF or BCF file - - annotations: - type: file - description: Bgzip-compressed file with annotations - - annotations_index: - type: file - description: Index of the annotations file - - header_lines: - type: file - description: Contains lines to append to the output VCF header - - rename_chrs: - type: file - description: Contains new and old chromosome names + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Query VCF or BCF file, can be either uncompressed or compressed + - index: + type: file + description: Index of the query VCF or BCF file + - annotations: + type: file + description: Bgzip-compressed file with annotations + - annotations_index: + type: file + description: Index of the annotations file + - - header_lines: + type: file + description: Contains lines to append to the output VCF header output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed annotated VCF file - pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Compressed annotated VCF file + pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 8cd87abc..3a5c4933 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -9,20 +9,21 @@ nextflow_process { tag "bcftools" tag "bcftools/annotate" - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") { config "./vcf.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -39,20 +40,21 @@ nextflow_process { } - test("sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output") { + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") { config "./vcf.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - []] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -68,20 +70,21 @@ nextflow_process { } } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") { config "./vcf_gz_index.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -101,20 +104,21 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") { config "./vcf_gz_index_csi.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -134,20 +138,21 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") { config "./vcf_gz_index_tbi.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -166,20 +171,21 @@ nextflow_process { } } - test("sarscov2 - [vcf, []], annotation, annotation_tbi, header - bcf_output") { + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") { config "./bcf.config" when { process { """ - input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - []]) - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = Channel.of( + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = Channel.of( '##INFO=', '##INFO=' ).collectFile(name:"headers.vcf", newLine:true) @@ -199,7 +205,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") { config "./vcf.config" options "-stub" @@ -207,13 +213,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -227,7 +234,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") { config "./vcf_gz_index.config" options "-stub" @@ -235,13 +242,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -256,7 +264,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") { config "./vcf_gz_index_csi.config" options "-stub" @@ -264,13 +272,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } @@ -285,7 +294,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") { config "./vcf_gz_index_tbi.config" options "-stub" @@ -293,13 +302,14 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)] - - input[1] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) - input[3] = [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] """ } } diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index 8fd8d11d..bac2224a 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -1,38 +1,5 @@ { - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_tbi": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi" - ] - ], - [ - - ], - [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-12T16:39:23.802873" - }, - "sarscov2 - [vcf, []] annotation, annotation_tbi, [] - vcf_output": { + "bcf": { "content": [ [ [ @@ -40,7 +7,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.bcf" ] ], [ @@ -51,9 +18,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:38:57.039285" + "timestamp": "2024-06-12T16:39:33.331888" }, - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index_csi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": { "content": [ [ [ @@ -84,9 +51,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:15.152697" + "timestamp": "2024-08-15T10:07:59.658031137" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -102,13 +69,25 @@ ], "2": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "3": [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ], "csi": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "tbi": [ @@ -131,9 +110,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:41.994785" + "timestamp": "2024-08-15T10:09:05.096883418" }, - "bcf": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": { "content": [ [ [ @@ -141,7 +120,19 @@ "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" ] ], [ @@ -152,9 +143,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:33.331888" + "timestamp": "2024-08-15T10:08:10.581301219" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_tbi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": { "content": [ { "0": [ @@ -167,13 +158,7 @@ ] ], "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "2": [ @@ -185,13 +170,7 @@ ], "tbi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "vcf": [ [ @@ -211,9 +190,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:40:13.835994" + "timestamp": "2024-08-15T10:08:43.975017625" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": { "content": [ [ [ @@ -223,6 +202,18 @@ }, "test_vcf.vcf.gz" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + ], [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" @@ -232,9 +223,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:38:48.368629" + "timestamp": "2024-08-15T10:08:21.354059092" }, - "sarscov2 - [vcf, tbi], annotation, annotation_tbi, [] - vcf_gz_index": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": { "content": [ [ [ @@ -246,15 +237,24 @@ ] ], [ - - ], + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:37.788393317" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": { + "content": [ [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_vcf.vcf.gz" ] ], [ @@ -265,9 +265,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:05.608108" + "timestamp": "2024-08-15T10:07:48.500746325" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -280,31 +280,31 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "2": [ + ], "3": [ "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ], "csi": [ + + ], + "tbi": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "tbi": [ - ], "vcf": [ [ @@ -324,9 +324,9 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:39:54.842082" + "timestamp": "2024-08-15T10:09:16.094918834" }, - "sarscov2 - [vcf, tbi] annotation, annotation_tbi, [] - vcf_gz_index_csi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -383,6 +383,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-06-12T16:40:04.074052" + "timestamp": "2024-08-15T10:08:54.366358502" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 6544e949..5c00b116 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_concat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index e2337eff..a94b28d8 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -11,18 +11,22 @@ process BCFTOOLS_CONCAT { tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("*.gz") , emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name } + def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n ") """ + ${create_input_index} + bcftools concat \\ --output ${prefix}.vcf.gz \\ $args \\ @@ -37,7 +41,7 @@ process BCFTOOLS_CONCAT { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : args.contains("--write-index") || args.contains("-W") ? "csi" : diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index eeeb2071..d2565b28 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -13,44 +13,68 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbi: - type: list - description: | - List containing 2 or more index files (optional) - e.g. [ 'file1.tbi', 'file2.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbi: + type: list + description: | + List containing 2 or more index files (optional) + e.g. [ 'file1.tbi', 'file2.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF concatenated output file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{vcf.gz}" + - ${prefix}.vcf.gz: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.tbi" + - ${prefix}.vcf.gz.tbi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.csi" + - ${prefix}.vcf.gz.csi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index cea386e3..cb4642b2 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_process { tag "bcftools/concat" - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") { config "./nextflow.config" @@ -41,7 +41,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { config "./vcf_gz_index.config" @@ -78,7 +78,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { config "./vcf_gz_index_csi.config" @@ -115,7 +115,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { config "./vcf_gz_index_tbi.config" @@ -153,7 +153,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], []]") { + test("homo_sapiens - [[vcf1, vcf2], []]") { config "./nextflow.config" @@ -181,7 +181,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { config "./nextflow.config" options "-stub" @@ -213,7 +213,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { config "./vcf_gz_index.config" options "-stub" @@ -246,7 +246,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { config "./vcf_gz_index_csi.config" options "-stub" @@ -279,7 +279,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { config "./vcf_gz_index_tbi.config" options "-stub" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 1182854f..09e87cd3 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -49,12 +49,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T08:09:13.734103412" + "timestamp": "2024-09-26T11:04:11.178539482" }, - "sarscov2 - [[vcf1, vcf2], []]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ { "0": [ @@ -94,12 +94,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:09.213249578" + "timestamp": "2024-09-26T11:03:08.765639958" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { "content": [ [ [ @@ -125,12 +125,12 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T08:08:23.981388325" + "timestamp": "2024-09-26T11:03:21.607274757" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -142,29 +142,29 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "2": [ + ], "3": [ "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ], "csi": [ + + ], + "tbi": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "tbi": [ - ], "vcf": [ [ @@ -180,12 +180,43 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T11:04:27.332133878" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:01:24.419027693" + "timestamp": "2024-09-26T11:03:36.575719606" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { + "homo_sapiens - [[vcf1, vcf2], []]": { "content": [ { "0": [ @@ -225,43 +256,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:03.597061078" + "timestamp": "2024-09-26T11:03:54.069826178" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { - "content": [ - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" - ] - ], - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.csi" - ] - ], - [ - - ], - [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-05T14:00:10.868487669" - }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ { "0": [ @@ -301,12 +301,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:14.836256897" + "timestamp": "2024-09-26T11:04:02.45346063" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { "content": [ [ [ @@ -332,12 +332,12 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:00:31.061411617" + "timestamp": "2024-09-26T11:03:44.618596639" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -349,29 +349,29 @@ ] ], "1": [ + + ], + "2": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "2": [ - ], "3": [ "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ], "csi": [ - - ], - "tbi": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "tbi": [ + ], "vcf": [ [ @@ -387,9 +387,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:01:35.209746508" + "timestamp": "2024-09-26T11:04:19.745768656" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index 71e39be3..5c00b116 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -1,4 +1,3 @@ -name: bcftools_merge channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index 2caf644e..2cf09a1d 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -12,67 +12,78 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: file - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbis: - type: file - description: | - List containing the tbi index files corresponding to the vcfs input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'genome' ] - - bed: - type: file - description: "(Optional) The bed regions to merge on" - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: file + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: "(Optional) The fasta reference file (only necessary for the `--gvcf + FILE` parameter)" + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: "(Optional) The fasta reference file index (only necessary for + the `--gvcf FILE` parameter)" + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: merged output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf}{,.gz}": + type: file + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: index of merged output - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: index of merged output + pattern: "*.{csi,tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 0c7dfa8f..5c00b116 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_norm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 97658267..bd7a2501 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -32,7 +32,7 @@ process BCFTOOLS_NORM { """ bcftools norm \\ --fasta-ref ${fasta} \\ - --output ${prefix}.${extension}\\ + --output ${prefix}.${extension} \\ $args \\ --threads $task.cpus \\ ${vcf} diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index a0cdeaf1..b6edeb4a 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -13,54 +13,70 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf' - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: | - An optional index of the VCF file (for when the VCF is compressed) - pattern: "*.vcf.gz.tbi" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf' + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: | + An optional index of the VCF file (for when the VCF is compressed) + pattern: "*.vcf.gz.tbi" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed + BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml index 1f7bb1ff..5c00b116 100644 --- a/modules/nf-core/bcftools/pluginsplit/environment.yml +++ b/modules/nf-core/bcftools/pluginsplit/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_pluginsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml index 64bfce0a..41f76658 100644 --- a/modules/nf-core/bcftools/pluginsplit/meta.yml +++ b/modules/nf-core/bcftools/pluginsplit/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginsplit" description: Split VCF by sample, creating single- or multi-sample VCFs. @@ -14,60 +13,83 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF file to split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: OPTIONAL - The index of the input VCF/BCF + pattern: "*.tbi" + - - samples: + type: file + description: | + A tab-separated file determining which samples should be in which output file + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file + Either this or a groups file should be given + pattern: "*" + - - groups: + type: file + description: | + A tab-separated file determining which samples should be in which output file(s) + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file(s) + Either this or a samples file should be given + pattern: "*" + - - regions: + type: file + description: A BED file containing regions to use + pattern: "*.bed" + - - targets: + type: file + description: A BED file containing regions to use (but streams rather than index-jumps) + pattern: "*.bed" +output: - vcf: - type: file - description: The VCF file to split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting VCF files from the split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: OPTIONAL - The index of the input VCF/BCF - pattern: "*.tbi" - - samples: - type: file - description: | - A tab-separated file determining which samples should be in which output file - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file - Either this or a groups file should be given - pattern: "*" - - groups: - type: file - description: | - A tab-separated file determining which samples should be in which output file(s) - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file(s) - Either this or a samples file should be given - pattern: "*" - - regions: - type: file - description: A BED file containing regions to use - pattern: "*.bed" - - targets: - type: file - description: A BED file containing regions to use (but streams rather than index-jumps) - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: TBI file + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf: - type: file - description: The resulting VCF files from the split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml index 303ef610..279b3205 100644 --- a/modules/nf-core/bcftools/query/meta.yml +++ b/modules/nf-core/bcftools/query/meta.yml @@ -1,5 +1,6 @@ name: bcftools_query -description: Extracts fields from VCF or BCF files and outputs them in user-defined format. +description: Extracts fields from VCF or BCF files and outputs them in user-defined + format. keywords: - query - variant calling @@ -13,48 +14,51 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be qeuried. - pattern: "*.{vcf.gz, vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be qeuried. + pattern: "*.{vcf.gz, vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. + pattern: "*.tbi" + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: BCFTools query output file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: BCFTools query output file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@drpatelh" diff --git a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff b/modules/nf-core/bcftools/reheader/bcftools-reheader.diff deleted file mode 100644 index e2c7a9a8..00000000 --- a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff +++ /dev/null @@ -1,36 +0,0 @@ -Changes in module 'nf-core/bcftools/reheader' ---- modules/nf-core/bcftools/reheader/main.nf -+++ modules/nf-core/bcftools/reheader/main.nf -@@ -13,6 +13,7 @@ - - output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf -+ tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions - - when: -@@ -59,8 +60,16 @@ - args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" : - args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : - "vcf" -+ def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" : -+ args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" : -+ args2.contains("--write-index") || args2.contains("-W") ? "csi" : -+ "" -+ def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" -+ def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" -+ - """ -- touch ${prefix}.${extension} -+ ${create_cmd} ${prefix}.${extension} -+ ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": -@@ -68,3 +77,4 @@ - END_VERSIONS - """ - } -+ - -************************************************************ diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 48fd72c9..5c00b116 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_reheader channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index d903cc0f..47e5344c 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -12,51 +12,60 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF/BCF file - pattern: "*.{vcf.gz,vcf,bcf}" - - header: - type: file - description: New header to add to the VCF - pattern: "*.{header.txt}" - - samples: - type: file - description: File containing sample names to update (one sample per line) - pattern: "*.{samples.txt}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Fasta index to update header sequences with - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - header: + type: file + description: New header to add to the VCF + pattern: "*.{header.txt}" + - samples: + type: file + description: File containing sample names to update (one sample per line) + pattern: "*.{samples.txt}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Fasta index to update header sequences with + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF with updated header, bgzipped per default - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF with updated header, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: Index of VCF with updated header - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: Index of VCF with updated header + pattern: "*.{csi,tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 2295ecfd..5c00b116 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index dfbddcba..f7a6eff1 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file to be sorted - pattern: "*.{vcf.gz,vcf,bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file to be sorted + pattern: "*.{vcf.gz,vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Sorted VCF file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 128fe204..93357b41 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -1,8 +1,6 @@ -name: bcftools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index 7ea2103e..655a61c5 100644 --- a/modules/nf-core/bcftools/stats/meta.yml +++ b/modules/nf-core/bcftools/stats/meta.yml @@ -13,58 +13,86 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' - - exons: - type: file - description: | - Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). - e.g. 'exons.tsv.gz' - - fasta: - type: file - description: | - Faidx indexed reference sequence file to determine INDEL context. - e.g. 'reference.fa' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. + pattern: "*.tbi" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exons: + type: file + description: | + Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). + e.g. 'exons.tsv.gz' + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Faidx indexed reference sequence file to determine INDEL context. + e.g. 'reference.fa' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: Text output file containing stats - pattern: "*_{stats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*stats.txt": + type: file + description: Text output file containing stats + pattern: "*_{stats.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml index 4b2a21df..5c00b116 100644 --- a/modules/nf-core/bcftools/view/environment.yml +++ b/modules/nf-core/bcftools/view/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml index 5eb1b196..aa7785f1 100644 --- a/modules/nf-core/bcftools/view/meta.yml +++ b/modules/nf-core/bcftools/view/meta.yml @@ -1,5 +1,6 @@ name: bcftools_view -description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF +description: View, subset and filter VCF or BCF files by position and filtering expression. + Convert between VCF and BCF keywords: - variant calling - view @@ -13,59 +14,74 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index 99707878..5683bc05 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index d7463e3d..6da54205 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -1,5 +1,6 @@ name: bedtools_merge -description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +description: combines overlapping or “book-ended” features in an interval file into + a single feature which spans all of the combined features. keywords: - bed - merge @@ -11,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Overlapped bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test index 95dba8e5..2959d6b9 100644 --- a/modules/nf-core/bedtools/merge/tests/main.nf.test +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] """ } diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index 87b2e425..5683bc05 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 7c915f5f..313698f1 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -11,35 +11,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BED/BEDGRAPH - pattern: "*.{bed|bedGraph}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: Sorted output file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Sorted output file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121..71e04c3d 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,5 @@ -name: cat_fastq channels: - conda-forge - bioconda - - defaults dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index b68e5f91..4364a389 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -4,8 +4,8 @@ process CAT_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c7..91ff2fb5 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index aec119a9..f8689a1c 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:30:39.816981" + "timestamp": "2024-10-19T20:02:07.519211144" }, "test_cat_fastq_single_end_same_name": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:35.229332" + "timestamp": "2024-10-19T20:02:31.618628921" }, "test_cat_fastq_single_end_single_file": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:34:00.058829" + "timestamp": "2024-10-19T20:02:57.904149581" }, "test_cat_fastq_paired_end_same_name": { "content": [ @@ -120,7 +120,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -135,15 +135,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:33:33.031555" + "timestamp": "2024-10-19T20:02:44.577183829" }, "test_cat_fastq_single_end - stub": { "content": [ @@ -158,7 +158,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -170,15 +170,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:28.244999" + "timestamp": "2024-10-19T20:03:10.603734777" }, "test_cat_fastq_paired_end_same_name - stub": { "content": [ @@ -196,7 +196,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -211,15 +211,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:57.070911" + "timestamp": "2024-10-19T20:03:46.041808828" }, "test_cat_fastq_single_end_same_name - stub": { "content": [ @@ -234,7 +234,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -246,15 +246,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:46.796254" + "timestamp": "2024-10-19T20:03:34.13865402" }, "test_cat_fastq_paired_end": { "content": [ @@ -272,7 +272,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -287,15 +287,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:02.270935" + "timestamp": "2024-10-19T20:02:19.64383573" }, "test_cat_fastq_paired_end - stub": { "content": [ @@ -313,7 +313,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -328,15 +328,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:37.807553" + "timestamp": "2024-10-19T20:03:22.597246066" }, "test_cat_fastq_single_end_single_file - stub": { "content": [ @@ -351,7 +351,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -363,14 +363,14 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:14:51.861264" + "timestamp": "2024-10-19T20:03:58.44849001" } } \ No newline at end of file diff --git a/modules/nf-core/deepvariant/README.md b/modules/nf-core/deepvariant/README.md deleted file mode 100644 index 9d1ceb34..00000000 --- a/modules/nf-core/deepvariant/README.md +++ /dev/null @@ -1,11 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/deepvariant/README.html) recipe is not fully working as expected. - -See https://github.com/bioconda/bioconda-recipes/issues/30310 and https://github.com/nf-core/modules/issues/1754 for more information. - -Hence, we are using the docker container provided by the authors of the tool: - -- [google/deepvariant](https://hub.docker.com/r/google/deepvariant) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/deepvariant) for convenience. diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml deleted file mode 100644 index 2327dd5f..00000000 --- a/modules/nf-core/deepvariant/meta.yml +++ /dev/null @@ -1,92 +0,0 @@ -name: deepvariant -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data -keywords: - - variant calling - - machine learning - - neural network -tools: - - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data - homepage: https://github.com/google/deepvariant - documentation: https://github.com/google/deepvariant - tool_dev_url: https://github.com/google/deepvariant - doi: "10.1038/nbt.4235" - licence: ["BSD-3-clause"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - interval: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" - - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" -authors: - - "@abhi18av" - - "@ramprasadn" -maintainers: - - "@abhi18av" - - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf similarity index 98% rename from modules/nf-core/deepvariant/main.nf rename to modules/nf-core/deepvariant/rundeepvariant/main.nf index 8d3d0911..7f99c53f 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf @@ -1,4 +1,4 @@ -process DEEPVARIANT { +process DEEPVARIANT_RUNDEEPVARIANT { tag "$meta.id" label 'process_high' diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml new file mode 100644 index 00000000..29b45ff9 --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml @@ -0,0 +1,122 @@ +name: deepvariant_rundeepvariant +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] + identifier: biotools:deepvariant +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: file containing intervals + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Tabix index file of compressed VCF + pattern: "*.vcf.gz.tbi" + - gvcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Tabix index file of compressed GVCF + pattern: "*.g.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@ramprasadn" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test similarity index 97% rename from modules/nf-core/deepvariant/tests/main.nf.test rename to modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test index 17765233..0790fb81 100644 --- a/modules/nf-core/deepvariant/tests/main.nf.test +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test @@ -1,9 +1,10 @@ nextflow_process { - name "Test Process DEEPVARIANT" + name "Test Process DEEPVARIANT_RUNDEEPVARIANT" script "../main.nf" - process "DEEPVARIANT" + process "DEEPVARIANT_RUNDEEPVARIANT" + tag "deepvariant/rundeepvariant" tag "deepvariant" tag "modules" tag "modules_nfcore" @@ -162,4 +163,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/deepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap similarity index 91% rename from modules/nf-core/deepvariant/tests/main.nf.test.snap rename to modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap index 04f87774..1ec351ee 100644 --- a/modules/nf-core/deepvariant/tests/main.nf.test.snap +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -78,15 +78,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:09:40.987117305" + "timestamp": "2024-08-29T11:36:27.325363" }, "homo_sapiens - [bam, bai] - fasta - fai": { "content": [ @@ -128,7 +128,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -167,15 +167,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:08:47.058887374" + "timestamp": "2024-08-29T11:34:41.779153" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": { "content": [ @@ -217,7 +217,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -256,15 +256,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:09:13.952808655" + "timestamp": "2024-08-29T11:35:16.993129" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": { "content": [ @@ -306,7 +306,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -345,14 +345,14 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-23T14:29:24.939680679" + "timestamp": "2024-08-29T11:35:52.23093" } -} +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/tests/nextflow-intervals.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config similarity index 70% rename from modules/nf-core/deepvariant/tests/nextflow-intervals.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config index 6d135f9f..78d8d598 100644 --- a/modules/nf-core/deepvariant/tests/nextflow-intervals.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = '--model_type=WGS ' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config similarity index 74% rename from modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config index 4be8986b..6d265292 100644 --- a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = '--model_type=WGS --haploid_contigs chr22' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/tests/nextflow.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config similarity index 75% rename from modules/nf-core/deepvariant/tests/nextflow.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config index d335d30b..77e355ca 100644 --- a/modules/nf-core/deepvariant/tests/nextflow.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS ' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml new file mode 100644 index 00000000..958b8e41 --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/rundeepvariant: + - modules/nf-core/deepvariant/rundeepvariant/** diff --git a/modules/nf-core/deepvariant/tests/tags.yml b/modules/nf-core/deepvariant/tests/tags.yml deleted file mode 100644 index 8e838c7b..00000000 --- a/modules/nf-core/deepvariant/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -deepvariant: - - modules/nf-core/deepvariant/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 3d98a08b..315f6dc6 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,7 +1,5 @@ -name: gawk channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index ca468929..7514246e 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -8,7 +8,7 @@ process GAWK { 'biocontainers/gawk:5.3.0' }" input: - tuple val(meta), path(input) + tuple val(meta), path(input, arity: '0..*') path(program_file) output: @@ -22,15 +22,19 @@ process GAWK { def args = task.ext.args ?: '' // args is used for the main arguments of the tool def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension()}" + suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files - program = program_file ? "-f ${program_file}" : "${args2}" + program = program_file ? "-f ${program_file}" : "${args2}" + lst_gz = input.collect{ it.getExtension().endsWith("gz") } + unzip = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\" + input_cmd = unzip ? "" : "${input}" """ + ${unzip} awk \\ ${args} \\ ${program} \\ - ${input} \\ + ${input_cmd} \\ > ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 2b6033b0..2da41405 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -16,34 +16,41 @@ tools: documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file - pattern: "*" - - program_file: - type: file - description: Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on + this file on the `ext.args2` or in the program file. + If the files have a `.gz` extension, they will be unzipped using `zcat`. + pattern: "*" + - - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't + wish to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix` - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${suffix}: + type: file + description: The output file - specify the name of this file using `ext.prefix` + and the extension using `ext.suffix` + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index fce82ca9..5952e9a2 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "modules_nfcore" tag "gawk" - test("convert fasta to bed") { + test("Convert fasta to bed") { config "./nextflow.config" when { @@ -31,7 +31,7 @@ nextflow_process { } } - test("convert fasta to bed with program file") { + test("Convert fasta to bed with program file") { config "./nextflow_with_program_file.config" when { @@ -53,4 +53,52 @@ nextflow_process { ) } } + + test("Extract first column from multiple files") { + config "./nextflow_with_program_file.config" + tag "test" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Unzip files before processing") { + config "./nextflow_with_program_file.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] + ] + input[1] = Channel.of('/^#CHROM/ { print \$1, \$10 }').collectFile(name:"column_header.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index 4f3a759c..d396f738 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "convert fasta to bed with program file": { + "Convert fasta to bed": { "content": [ { "0": [ @@ -28,11 +28,11 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T15:20:02.495430346" + "timestamp": "2024-10-19T13:14:02.347809811" }, - "convert fasta to bed": { + "Convert fasta to bed with program file": { "content": [ { "0": [ @@ -61,8 +61,74 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T15:19:53.291809648" + "timestamp": "2024-10-19T13:14:11.894616209" + }, + "Extract first column from multiple files": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:04:47.729300129" + }, + "Unzip files before processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:08:19.533527657" } -} \ No newline at end of file +} diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml index 1c875ce0..b47bbdbb 100644 --- a/modules/nf-core/gfastats/environment.yml +++ b/modules/nf-core/gfastats/environment.yml @@ -1,7 +1,5 @@ -name: gfastats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gfastats=1.3.6 diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml index d0e97a8f..a6213433 100644 --- a/modules/nf-core/gfastats/meta.yml +++ b/modules/nf-core/gfastats/meta.yml @@ -16,56 +16,67 @@ tools: documentation: "https://github.com/vgl-hub/gfastats/tree/main/instructions" tool_dev_url: "https://github.com/vgl-hub/gfastats" doi: "10.1093/bioinformatics/btac460" - licence: "['MIT']" + licence: ["MIT"] + identifier: biotools:gfastats input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly file - pattern: "*.{fasta,fastq,gfa}(.gz)?" - - out_fmt: - type: string - description: Output format (fasta, fastq, gfa) - - genome_size: - type: integer - description: estimated genome size (bp) for NG* statistics (optional). - - target: - type: string - description: target specific sequence by header, optionally with coordinates (optional). - - agpfile: - type: file - description: converts input agp to path and replaces existing paths. - - include_bed: - type: file - description: generates output on a subset list of headers or coordinates in 0-based bed format. - - exclude_bed: - type: file - description: opposite of --include-bed. They can be combined (no coordinates). - - instructions: - type: file - description: set of instructions provided as an ordered list. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly file + pattern: "*.{fasta,fastq,gfa}(.gz)?" + - - out_fmt: + type: string + description: Output format (fasta, fastq, gfa) + - - genome_size: + type: integer + description: estimated genome size (bp) for NG* statistics (optional). + - - target: + type: string + description: target specific sequence by header, optionally with coordinates + (optional). + - - agpfile: + type: file + description: converts input agp to path and replaces existing paths. + - - include_bed: + type: file + description: generates output on a subset list of headers or coordinates in + 0-based bed format. + - - exclude_bed: + type: file + description: opposite of --include-bed. They can be combined (no coordinates). + - - instructions: + type: file + description: set of instructions provided as an ordered list. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly_summary: - type: file - description: Assembly summary statistics file - pattern: "*.assembly_summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly_summary": + type: file + description: Assembly summary statistics file + pattern: "*.assembly_summary" - assembly: - type: file - description: The assembly as modified by gfastats - pattern: "*.{fasta,fastq,gfa}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_fmt}.gz": + type: file + description: The assembly as modified by gfastats + pattern: "*.{fasta,fastq,gfa}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/glnexus/glnexus.diff b/modules/nf-core/glnexus/glnexus.diff index d7324596..8684c709 100644 --- a/modules/nf-core/glnexus/glnexus.diff +++ b/modules/nf-core/glnexus/glnexus.diff @@ -3,8 +3,8 @@ Changes in module 'nf-core/glnexus' Changes in 'glnexus/main.nf': --- modules/nf-core/glnexus/main.nf +++ modules/nf-core/glnexus/main.nf -@@ -3,12 +3,11 @@ - label 'process_medium' +@@ -3,9 +3,7 @@ + label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -14,26 +14,8 @@ Changes in 'glnexus/main.nf': input: tuple val(meta), path(gvcfs) -+ tuple val(meta2), path(bed) - - output: - tuple val(meta), path("*.bcf"), emit: bcf -@@ -20,6 +19,7 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -+ def regions = bed ? "--bed ${bed}" : "" - - // Make list of GVCFs to merge - def input = gvcfs.collect { it.toString() } -@@ -33,6 +33,7 @@ - glnexus_cli \\ - --threads $task.cpus \\ - --mem-gbytes $avail_mem \\ -+ $regions \\ - $args \\ - ${input.join(' ')} \\ - > ${prefix}.bcf 'modules/nf-core/glnexus/environment.yml' is unchanged +'modules/nf-core/glnexus/tests/main.nf.test.snap' is unchanged +'modules/nf-core/glnexus/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 77754301..59857115 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -1,6 +1,6 @@ process GLNEXUS { tag "$meta.id" - label 'process_medium' + label 'process_high' conda "${moduleDir}/environment.yml" container "pacbio/glnexus:v1.4.3" // Biocontainers version does not have jemalloc diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index a79fc63c..8f18bf3f 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -23,6 +23,15 @@ input: type: list description: Input genomic vcf files pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing regions information + e.g. [ id:'test' ] + - bed: + type: list + description: Input BED file + pattern: "*.bed" output: - bcf: - meta: diff --git a/modules/nf-core/glnexus/tests/main.nf.test b/modules/nf-core/glnexus/tests/main.nf.test new file mode 100644 index 00000000..79f7adc8 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test @@ -0,0 +1,97 @@ +nextflow_process { + + name "Test Process GLNEXUS" + script "../main.nf" + process "GLNEXUS" + + tag "modules" + tag "modules_nfcore" + tag "glnexus" + + test("vcfs, []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ] + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/glnexus/tests/main.nf.test.snap b/modules/nf-core/glnexus/tests/main.nf.test.snap new file mode 100644 index 00000000..3d2e13f0 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test.snap @@ -0,0 +1,101 @@ +{ + "vcfs, bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-29T12:17:01.253378301" + }, + "vcfs, bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-29T12:16:53.859544065" + }, + "vcfs, []": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions": [ + "versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-29T12:13:03.068397129" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index dfc02a7b..c7794856 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,8 +1,6 @@ -name: gunzip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0..9066c035 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml index 41e8fe9f..dc6476b7 100644 --- a/modules/nf-core/minimap2/align/environment.yml +++ b/modules/nf-core/minimap2/align/environment.yml @@ -1,9 +1,6 @@ -name: minimap2_align - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml index 8996f881..a4cfc891 100644 --- a/modules/nf-core/minimap2/align/meta.yml +++ b/modules/nf-core/minimap2/align/meta.yml @@ -14,62 +14,77 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_ref'] - - reference: - type: file - description: | - Reference database in FASTA format. - - bam_format: - type: boolean - description: Specify that output should be in BAM format - - bam_index_extension: - type: string - description: BAM alignment index extension (e.g. "bai") - - cigar_paf_format: - type: boolean - description: Specify that output CIGAR should be in PAF format - - cigar_bam: - type: boolean - description: | - Write CIGAR with >65535 ops at the CG tag. This is recommended when - doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_ref'] + - reference: + type: file + description: | + Reference database in FASTA format. + - - bam_format: + type: boolean + description: Specify that output should be in BAM format + - - bam_index_extension: + type: string + description: BAM alignment index extension (e.g. "bai") + - - cigar_paf_format: + type: boolean + description: Specify that output CIGAR should be in PAF format + - - cigar_bam: + type: boolean + description: | + Write CIGAR with >65535 ops at the CG tag. This is recommended when + doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - bam: - type: file - description: Alignment in BAM format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Alignment in BAM format + pattern: "*.bam" - index: - type: file - description: BAM alignment index - pattern: "*.bam.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.${bam_index_extension}": + type: file + description: BAM alignment index + pattern: "*.bam.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" - "@sofstam" diff --git a/modules/nf-core/minimap2/index/environment.yml b/modules/nf-core/minimap2/index/environment.yml index 8a912a12..d1c1b471 100644 --- a/modules/nf-core/minimap2/index/environment.yml +++ b/modules/nf-core/minimap2/index/environment.yml @@ -1,7 +1,5 @@ -name: minimap2_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.28 diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml index 1d29e3f2..57c80e29 100644 --- a/modules/nf-core/minimap2/index/meta.yml +++ b/modules/nf-core/minimap2/index/meta.yml @@ -11,30 +11,33 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Minimap2 fasta index. - pattern: "*.mmi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mmi": + type: file + description: Minimap2 fasta index. + pattern: "*.mmi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml index 95074539..1343a05b 100644 --- a/modules/nf-core/modkit/pileup/environment.yml +++ b/modules/nf-core/modkit/pileup/environment.yml @@ -1,7 +1,5 @@ -name: modkit_pileup channels: - conda-forge - bioconda - - defaults dependencies: - ont-modkit=0.3.0 diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml index eb2875f4..2f274d0c 100644 --- a/modules/nf-core/modkit/pileup/meta.yml +++ b/modules/nf-core/modkit/pileup/meta.yml @@ -6,67 +6,83 @@ keywords: - long-read tools: - "modkit": - description: A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data + description: A bioinformatics tool for working with modified bases in Oxford Nanopore + sequencing data homepage: https://github.com/nanoporetech/modkit documentation: https://github.com/nanoporetech/modkit tool_dev_url: https://github.com/nanoporetech/modkit licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Associated index file for BAM - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing BED file information - e.g. `[ id:'regions' ]` - - bed: - type: file - description: - BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the - file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Associated index file for BAM + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference sequence in FASTA format. Required for motif (e.g. CpG) + filtering + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing BED file information + e.g. `[ id:'regions' ]` + - bed: + type: file + description: BED file that will restrict threshold estimation and pileup results + to positions overlapping intervals in the file + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: bedMethyl output file(s) - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: bedMethyl output file(s) + pattern: "*.bed" - bedgraph: - type: file - description: bedgraph output files - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bedgraph": + type: file + description: bedgraph output files + pattern: "*.bedgraph" - log: - type: file - description: File for debug logs to be written to - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.log": + type: file + description: File for debug logs to be written to + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Michal-Babins" - "@fellen31" diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index bcb9d64a..e9379873 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,8 +1,6 @@ -name: mosdepth channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 9caaf2cd..dc783c90 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -12,91 +12,161 @@ tools: documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 licence: ["MIT"] + identifier: biotools:mosdepth input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index for BAM/CRAM file - pattern: "*.{bai,crai}" - - bed: - type: file - description: BED file with intersected intervals - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - global_txt: - type: file - description: Text file with global cumulative coverage distribution - pattern: "*.{global.dist.txt}" - - regions_txt: - type: file - description: Text file with region cumulative coverage distribution - pattern: "*.{region.dist.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.global.dist.txt": + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" - summary_txt: - type: file - description: Text file with summary mean depths per chromosome and regions - pattern: "*.{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - regions_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.region.dist.txt": + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - per_base_d4: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.d4": + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" - per_base_bed: - type: file - description: BED file with per-base coverage - pattern: "*.{per-base.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz": + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" - per_base_csi: - type: file - description: Index file for BED file with per-base coverage - pattern: "*.{per-base.bed.gz.csi}" - - per_base_d4: - type: file - description: D4 file with per-base coverage - pattern: "*.{per-base.d4}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz.csi": + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" - regions_bed: - type: file - description: BED file with per-region coverage - pattern: "*.{regions.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz": + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" - regions_csi: - type: file - description: Index file for BED file with per-region coverage - pattern: "*.{regions.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz.csi": + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" - quantized_bed: - type: file - description: BED file with binned coverage - pattern: "*.{quantized.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz": + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" - quantized_csi: - type: file - description: Index file for BED file with binned coverage - pattern: "*.{quantized.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz.csi": + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" - thresholds_bed: - type: file - description: BED file with the number of bases in each region that are covered at or above each threshold - pattern: "*.{thresholds.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz": + type: file + description: BED file with the number of bases in each region that are covered + at or above each threshold + pattern: "*.{thresholds.bed.gz}" - thresholds_csi: - type: file - description: Index file for BED file with threshold coverage - pattern: "*.{thresholds.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz.csi": + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index 21eebc1f..0b3c860d 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -40,9 +40,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -65,13 +65,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -93,13 +93,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -122,8 +122,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -148,8 +148,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -174,9 +174,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -200,9 +200,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -225,9 +225,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-10-02T17:52:09.185842" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index e6cc6d63..50c3c9e0 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "paraphase" description: "HiFi-based caller for highly homologous genes" @@ -14,73 +13,96 @@ tools: tool_dev_url: "https://github.com/PacificBiosciences/paraphase" doi: "10.1016/j.ajhg.2023.01.001" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing config information - e.g. [ id:'config' ] - - config: - type: file - description: Config file - pattern: "*.yaml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index of BAM file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing config information + e.g. [ id:'config' ] + - config: + type: file + description: Config file + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.json": + type: file + description: Summary of haplotype and variant calls + pattern: "*.paraphase.json" - bam: - type: file - description: (re)aligned BAM file - pattern: "*.paraphase.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam": + type: file + description: (re)aligned BAM file + pattern: "*.paraphase.bam" - bai: - type: file - description: Index of (re)aligned BAM file - pattern: "*.paraphase.bam.bai" - - json: - type: file - description: Summary of haplotype and variant calls - pattern: "*.paraphase.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam.bai": + type: file + description: Index of (re)aligned BAM file + pattern: "*.paraphase.bam.bai" - vcf: - type: file - description: compressed VCF file(s) per gene - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz: + type: file + description: compressed VCF file(s) per gene + pattern: "*.vcf.gz" - vcf_index: - type: file - description: compressed VCF file index - pattern: "*.vcf.gz.{tbi,csi}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}: + type: file + description: compressed VCF file index + pattern: "*.vcf.gz.{tbi,csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index f8450fa5..62054fc9 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,10 +1,8 @@ -name: samtools_faidx - +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index bdcdbc95..28c0a81c 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index f3c25de2..6721b2cb 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -14,47 +14,62 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fa: - type: file - description: FASTA file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3223b72b..1bbb3ec2 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:14.779784761" + "timestamp": "2024-09-16T07:57:47.450887871" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:20.256633877" + "timestamp": "2024-09-16T07:58:04.804905659" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -142,15 +142,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:25.632577273" + "timestamp": "2024-09-16T07:58:23.831268154" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -189,15 +189,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:31.058424849" + "timestamp": "2024-09-16T07:58:35.600243706" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -236,14 +236,14 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:36.479929617" + "timestamp": "2024-09-16T07:58:54.705460167" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index 4455904e..62054fc9 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -1,8 +1,8 @@ -name: samtools_fastq +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 6796c02b..136744d5 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/meta.yml b/modules/nf-core/samtools/fastq/meta.yml index c4002a45..c15a0b6f 100644 --- a/modules/nf-core/samtools/fastq/meta.yml +++ b/modules/nf-core/samtools/fastq/meta.yml @@ -15,45 +15,69 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - interleave: - type: boolean - description: Set true for interleaved fastq file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - interleave: + type: boolean + description: Set true for interleaved fastq file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files. - pattern: "*_{1,2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_{1,2}.fastq.gz": + type: file + description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 + flag set in separate files. + pattern: "*_{1,2}.fastq.gz" - interleaved: - type: file - description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file. - pattern: "*_interleaved.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_interleaved.fastq": + type: file + description: Compressed FASTQ file with reads with either the READ1 or READ2 + flag set in a combined file. Needs collated input file. + pattern: "*_interleaved.fastq.gz" - singleton: - type: file - description: Compressed FASTQ file with singleton reads - pattern: "*_singleton.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_singleton.fastq.gz": + type: file + description: Compressed FASTQ file with singleton reads + pattern: "*_singleton.fastq.gz" - other: - type: file - description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset - pattern: "*_other.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_other.fastq.gz": + type: file + description: Compressed FASTQ file with reads with either both READ1 and READ2 + flags set or unset + pattern: "*_other.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@suzannejin" diff --git a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap index 1ba09d3a..10e5cd3d 100644 --- a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap @@ -93,26 +93,26 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:40.362380302" + "timestamp": "2024-09-16T08:00:41.44921616" }, "bam_verinterleave_sions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:45.632731997" + "timestamp": "2024-09-16T08:00:56.47781168" }, "bam_singleton": { "content": [ diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index 38f1ebab..62054fc9 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -1,8 +1,8 @@ -name: samtools_import +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/import/main.nf b/modules/nf-core/samtools/import/main.nf index 954a8052..e0a51c03 100644 --- a/modules/nf-core/samtools/import/main.nf +++ b/modules/nf-core/samtools/import/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samtools/import/meta.yml b/modules/nf-core/samtools/import/meta.yml index 9002e092..5c98b8be 100644 --- a/modules/nf-core/samtools/import/meta.yml +++ b/modules/nf-core/samtools/import/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "samtools_import" description: converts FASTQ files to unmapped SAM/BAM/CRAM @@ -18,38 +17,53 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq data to be converted to SAM/BAM/CRAM - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: fastq data to be converted to SAM/BAM/CRAM + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sam: - type: file - description: SAM file - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.sam": + type: file + description: SAM file + pattern: "*.sam" - bam: - type: file - description: Unaligned BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Unaligned BAM file + pattern: "*.bam" - cram: - type: file - description: Unaligned CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.cram": + type: file + description: Unaligned CRAM file + pattern: "*.cram" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/import/tests/main.nf.test b/modules/nf-core/samtools/import/tests/main.nf.test index d029ca70..9c7ce5d9 100644 --- a/modules/nf-core/samtools/import/tests/main.nf.test +++ b/modules/nf-core/samtools/import/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]) """ } @@ -42,8 +42,8 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]) """ } @@ -67,7 +67,7 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ]) """ } diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 260d516b..62054fc9 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,8 @@ -name: samtools_index +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b..31175610 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03..db8df0d5 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199c..72d65e81 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:53.9057" + "timestamp": "2024-09-16T08:21:25.261127166" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-09-16T08:21:12.653194876" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-09-16T08:21:01.854932651" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-09-16T08:20:51.485364222" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-09-16T08:20:40.518873972" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 67712a68..b08fc5f6 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,20 +4,21 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) - val(index_type) - + output: - tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam - tuple val(meta), path("${prefix}.cram") , optional:true, emit: cram - tuple val(meta), path("*.${index_type}"), optional:true, emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam + tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram + tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.crai") , optional:true, emit: crai + path "versions.yml" , emit: versions + when: task.ext.when == null || task.ext.when @@ -26,15 +27,15 @@ process SAMTOOLS_MERGE { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() - def reference = fasta ? "--reference ${fasta}" : "" def input = (input_files.collect().size() > 1) ? input_files.sort { it.name } : input_files + def reference = fasta ? "--reference ${fasta}" : "" """ samtools \\ merge \\ --threads ${task.cpus-1} \\ $args \\ ${reference} \\ - ${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_type} \\ + ${prefix}.${file_type}##idx##${prefix}.${file_type}.bai \\ $input cat <<-END_VERSIONS > versions.yml @@ -47,9 +48,10 @@ process SAMTOOLS_MERGE { def args = task.ext.args ?: '' prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() - def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.${index_type}" : "" + def index_type = "bai" + def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : "" """ - touch ${prefix}.${file_type}.${index_type} + touch ${prefix}.${file_type} ${index} cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff index e1402bb4..e4e6434d 100644 --- a/modules/nf-core/samtools/merge/samtools-merge.diff +++ b/modules/nf-core/samtools/merge/samtools-merge.diff @@ -3,68 +3,51 @@ Changes in module 'nf-core/samtools/merge' Changes in 'samtools/merge/main.nf': --- modules/nf-core/samtools/merge/main.nf +++ modules/nf-core/samtools/merge/main.nf -@@ -4,21 +4,20 @@ - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : -- 'biocontainers/samtools:1.21--h50ea8bc_0' }" -+ 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : -+ 'biocontainers/samtools:1.20--h50ea8bc_0' }" +@@ -8,14 +8,14 @@ + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: - tuple val(meta), path(input_files, stageAs: "?/*") + tuple val(meta), path(input_files) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) -- -+ val(index_type) -+ + output: -- tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam -- tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram + tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam + tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram - tuple val(meta), path("*.csi") , optional:true, emit: csi -- tuple val(meta), path("*.crai") , optional:true, emit: crai -- path "versions.yml" , emit: versions -- -+ tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam -+ tuple val(meta), path("${prefix}.cram") , optional:true, emit: cram -+ tuple val(meta), path("*.${index_type}"), optional:true, emit: index -+ path "versions.yml" , emit: versions ++ tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.crai") , optional:true, emit: crai + path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when -@@ -28,14 +27,15 @@ +@@ -27,6 +27,7 @@ + def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() - def reference = fasta ? "--reference ${fasta}" : "" + def input = (input_files.collect().size() > 1) ? input_files.sort { it.name } : input_files + def reference = fasta ? "--reference ${fasta}" : "" """ samtools \\ - merge \\ +@@ -34,8 +35,8 @@ --threads ${task.cpus-1} \\ $args \\ ${reference} \\ - ${prefix}.${file_type} \\ - $input_files -+ ${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_type} \\ ++ ${prefix}.${file_type}##idx##${prefix}.${file_type}.bai \\ + $input cat <<-END_VERSIONS > versions.yml "${task.process}": -@@ -47,10 +47,9 @@ +@@ -47,7 +48,7 @@ def args = task.ext.args ?: '' prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() - def index_type = file_type == "bam" ? "csi" : "crai" -- def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : "" -+ def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.${index_type}" : "" ++ def index_type = "bai" + def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : "" """ -- touch ${prefix}.${file_type} -+ touch ${prefix}.${file_type}.${index_type} - ${index} - - cat <<-END_VERSIONS > versions.yml + touch ${prefix}.${file_type} 'modules/nf-core/samtools/merge/environment.yml' is unchanged 'modules/nf-core/samtools/merge/tests/tags.yml' is unchanged diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 36a12eab..62054fc9 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,8 @@ -name: samtools_sort +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099..caf3c61a 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,19 +4,19 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0e..a9dbec5a 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/samtools-sort.diff b/modules/nf-core/samtools/sort/samtools-sort.diff new file mode 100644 index 00000000..1a6d1649 --- /dev/null +++ b/modules/nf-core/samtools/sort/samtools-sort.diff @@ -0,0 +1,22 @@ +Changes in module 'nf-core/samtools/sort' +'modules/nf-core/samtools/sort/meta.yml' is unchanged +'modules/nf-core/samtools/sort/main.nf' is unchanged +Changes in 'samtools/sort/environment.yml': +--- modules/nf-core/samtools/sort/environment.yml ++++ modules/nf-core/samtools/sort/environment.yml +@@ -1,6 +1,8 @@ ++name: samtools_sort + channels: + - conda-forge + - bioconda ++ - defaults + dependencies: + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 + +'modules/nf-core/samtools/sort/tests/tags.yml' is unchanged +'modules/nf-core/samtools/sort/tests/nextflow_cram.config' is unchanged +'modules/nf-core/samtools/sort/tests/main.nf.test.snap' is unchanged +'modules/nf-core/samtools/sort/tests/nextflow.config' is unchanged +'modules/nf-core/samtools/sort/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index c2ea9c72..b05e6691 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -39,6 +39,40 @@ nextflow_process { } } + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + test("cram") { config "./nextflow_cram.config" @@ -98,6 +132,36 @@ nextflow_process { } } + test("multiple bam - stub") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("cram - stub") { options "-stub" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d1..469891fe 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-09-16T08:49:58.207549273" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ] ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -84,15 +84,15 @@ ] ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-09-16T08:50:08.630951018" }, "cram - stub": { "content": [ @@ -122,7 +122,7 @@ ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ @@ -149,15 +149,110 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" + }, + "multiple bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:55.479443" + }, + "multiple bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" }, "bam": { "content": [ @@ -167,7 +262,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +275,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.09.0" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-10-08T11:59:46.372244" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 150c3777..62054fc9 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,8 +1,8 @@ -name: samtools_view +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index dc611448..37e05cec 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 27be60d0..caa7b015 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -15,77 +15,120 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) - pattern: "*.{.bai,.csi,.crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) + pattern: "*.{.bai,.csi,.crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: optional filtered/converted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: optional filtered/converted BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/converted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: optional filtered/converted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/converted SAM file - pattern: "*.{sam}" - # bai, csi, and crai are created with `--write-index` + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: optional filtered/converted SAM file + pattern: "*.{sam}" - bai: - type: file - description: optional BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.bai: + type: file + description: optional BAM file index + pattern: "*.{bai}" - csi: - type: file - description: optional tabix BAM file index - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.csi: + type: file + description: optional tabix BAM file index + pattern: "*.{csi}" - crai: - type: file - description: optional CRAM file index - pattern: "*.{crai}" - # unselected and unselected_index are created when passing a qname + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.crai: + type: file + description: optional CRAM file index + pattern: "*.{crai}" - unselected: - type: file - description: optional file with unselected alignments - pattern: "*.unselected.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" - unselected_index: - type: file - description: index for the "unselected" file - pattern: "*.unselected.{bai,csi,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}.{bai,csi,crsi}: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6bcce9fe..63849b03 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -56,14 +56,14 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:20.390692583" + "timestamp": "2024-09-16T09:26:24.461775464" }, "cram_to_bam_index_cram": { "content": [ @@ -169,6 +169,16 @@ }, "timestamp": "2024-02-12T19:37:56.490286" }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_csi": { "content": [ [ @@ -208,14 +218,14 @@ "cram_to_bam_index_qname_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:15.007493874" + "timestamp": "2024-09-16T09:25:51.953436682" }, "cram_to_bam_bam": { "content": [ @@ -240,14 +250,14 @@ "cram_to_bam_index_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:09.472376824" + "timestamp": "2024-09-16T09:25:14.475388399" }, "cram_to_bam_bai": { "content": [ @@ -264,14 +274,14 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:04.080050906" + "timestamp": "2024-09-16T09:24:49.673441798" }, "cram_bam": { "content": [ @@ -378,14 +388,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:52.978954857" + "timestamp": "2024-09-16T09:23:27.151650338" }, "cram_to_bam_index_qname_cram": { "content": [ @@ -450,14 +460,24 @@ "cram_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:24:12.95416913" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" }, - "timestamp": "2024-05-28T15:42:58.400776109" + "timestamp": "2024-02-12T19:38:23.322874" }, "bam_sam": { "content": [ diff --git a/modules/nf-core/severus/meta.yml b/modules/nf-core/severus/meta.yml index 844eee44..8ada3548 100644 --- a/modules/nf-core/severus/meta.yml +++ b/modules/nf-core/severus/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "severus" -description: Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT) +description: Severus is a somatic structural variation (SV) caller for long reads + (both PacBio and ONT) keywords: - structural - variation @@ -16,112 +16,201 @@ tools: tool_dev_url: "https://github.com/KolmogorovLab/Severus" doi: "10.1101/2024.03.22.24304756" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - target_input: - type: file - description: path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed) - pattern: "*.{bam,cram}" - - target_index: - type: file - description: path to one or multiple target BAM/CRAM index files - pattern: "*.{bai,crai,csi}" - - control_input: - type: file - description: path to the control BAM/CRAM file (e.g. normal, must be indexed) - pattern: "*.{bam,cram}" - - control_index: - type: file - description: path to the control BAM/CRAM file index - pattern: "*.{bai,crai,csi}" - - vcf: - type: file - description: path to vcf file used for phasing (if using haplotype specific SV calling - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing tandem repeat regions information - e.g. `[ id:'hg38']` - - bed: - type: file - description: path to bed file for tandem repeat regions (must be ordered) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - target_input: + type: file + description: path to one or multiple target BAM/CRAM files (e.g. tumor, must + be indexed) + pattern: "*.{bam,cram}" + - target_index: + type: file + description: path to one or multiple target BAM/CRAM index files + pattern: "*.{bai,crai,csi}" + - control_input: + type: file + description: path to the control BAM/CRAM file (e.g. normal, must be indexed) + pattern: "*.{bam,cram}" + - control_index: + type: file + description: path to the control BAM/CRAM file index + pattern: "*.{bai,crai,csi}" + - vcf: + type: file + description: path to vcf file used for phasing (if using haplotype specific + SV calling + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing tandem repeat regions information + e.g. `[ id:'hg38']` + - bed: + type: file + description: path to bed file for tandem repeat regions (must be ordered) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: Severus log file - pattern: "${prefix}/severus.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus.log: + type: file + description: Severus log file + pattern: "${prefix}/severus.log" - read_qual: - type: file - description: Severus read_qual file - pattern: "${prefix}/read_qual.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_qual.txt: + type: file + description: Severus read_qual file + pattern: "${prefix}/read_qual.txt" - breakpoints_double: - type: file - description: Severus breakpoints_double file - pattern: "${prefix}/breakpoints_double.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/breakpoints_double.csv: + type: file + description: Severus breakpoints_double file + pattern: "${prefix}/breakpoints_double.csv" - read_alignments: - type: file - description: read alignments file - pattern: "${prefix}/read_alignments" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_alignments: + type: file + description: read alignments file + pattern: "${prefix}/read_alignments" - read_ids: - type: file - description: read IDs for support reads - pattern: "${prefix}/read_ids" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_ids.csv: + type: file + description: read IDs for support reads + pattern: "${prefix}/read_ids" - collapsed_dup: - type: file - description: a bed file with identified collapsed duplication regions - pattern: "${prefix}/severus_collaped_dup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_collaped_dup.bed: + type: file + description: a bed file with identified collapsed duplication regions + pattern: "${prefix}/severus_collaped_dup" - loh: - type: file - description: a bed file with predicted LOH regions - pattern: "${prefix}/severus_LOH.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_LOH.bed: + type: file + description: a bed file with predicted LOH regions + pattern: "${prefix}/severus_LOH.bed" - all_vcf: - type: file - description: VCF file with all SVs (somatic + germline) - pattern: "${prefix}/all_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/severus_all.vcf: + type: file + description: VCF file with all SVs (somatic + germline) + pattern: "${prefix}/all_SVs/severus_all.vcf" - all_breakpoints_clusters_list: - type: file - description: Severus breakpoints clusters list file - pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus breakpoints clusters list file + pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" - all_breakpoints_clusters: - type: file - description: Severus breakpoints clusters file - pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters.tsv: + type: file + description: Severus breakpoints clusters file + pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" - all_plots: - type: file - description: Severus plots - pattern: "${prefix}/all_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/plots/severus_*.html: + type: file + description: Severus plots + pattern: "${prefix}/all_SVs/plots/*.html" - somatic_vcf: - type: file - description: VCF file with somatic SVs - pattern: "${prefix}/somatic_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/severus_all.vcf: + type: file + description: VCF file with somatic SVs + pattern: "${prefix}/somatic_SVs/severus_all.vcf" - somatic_breakpoints_clusters_list: - type: file - description: Severus somatic breakpoints clusters list file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus somatic breakpoints clusters list file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" - somatic_breakpoints_clusters: - type: file - description: Severus somatic breakpoints clusters file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters.tsv: + type: file + description: Severus somatic breakpoints clusters file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" - somatic_plots: - type: file - description: Severus somatic plots - pattern: "${prefix}/somatic_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/plots/severus_*.html: + type: file + description: Severus somatic plots + pattern: "${prefix}/somatic_SVs/plots/*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/severus/tests/main.nf.test b/modules/nf-core/severus/tests/main.nf.test index 1b85a109..ab700a4c 100644 --- a/modules/nf-core/severus/tests/main.nf.test +++ b/modules/nf-core/severus/tests/main.nf.test @@ -7,7 +7,6 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "severus" - tag "deepvariant" test("homo_sapiens - [ bam, bai, [], [], [] ], [[],[]]") { @@ -206,4 +205,4 @@ nextflow_process { } -} \ No newline at end of file +} diff --git a/modules/nf-core/severus/tests/main.nf.test.snap b/modules/nf-core/severus/tests/main.nf.test.snap index 0dc24142..a5c527eb 100644 --- a/modules/nf-core/severus/tests/main.nf.test.snap +++ b/modules/nf-core/severus/tests/main.nf.test.snap @@ -268,7 +268,12 @@ ] ], "7": [ - + [ + { + "id": "test" + }, + "severus_all.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "8": [ [ @@ -314,7 +319,12 @@ ] ], "all_vcf": [ - + [ + { + "id": "test" + }, + "severus_all.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "breakpoints_double": [ [ @@ -409,9 +419,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nextflow": "24.04.2" }, - "timestamp": "2024-09-11T19:09:18.357545892" + "timestamp": "2024-07-10T12:00:07.296601854" }, "homo_sapiens - [ bam, bai, bam, bai, [] ], [[],[]]": { "content": [ diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml index db8f3f69..b3d97d0e 100644 --- a/modules/nf-core/sniffles/environment.yml +++ b/modules/nf-core/sniffles/environment.yml @@ -1,7 +1,5 @@ -name: sniffles channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::sniffles=2.0.7 + - bioconda::sniffles=2.4 diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml index c8b2da7d..b52d45a3 100644 --- a/modules/nf-core/sniffles/meta.yml +++ b/modules/nf-core/sniffles/meta.yml @@ -11,59 +11,88 @@ tools: documentation: https://github.com/fritzsedlazeck/Sniffles#readme tool_dev_url: https://github.com/fritzsedlazeck/Sniffles licence: ["MIT"] + identifier: biotools:sniffles input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: file - description: BAM or SNF file - pattern: "*.{bam, snf}" - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: | - Reference database in FASTA format - - meta3: - type: map - description: | - Groovy Map containing tandem repeat file information - e.g. [ id:'tandem_repeats' ] - - tandem_file: - type: file - description: | - Tandem repeats file in BED format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: A single .bam/.cram file - OR - one or more .snf files - OR - a + single .tsv file containing a list of .snf files and optional sample ids as + input + pattern: "*.{bam,cram,snf,tsv}" + - index: + type: file + description: Index of BAM/CAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: | + Reference database in FASTA format + - - meta3: + type: map + description: | + Groovy Map containing tandem repeat information + e.g. [ id:'hg38' ] + - tandem_file: + type: file + description: Tandem repeat file + pattern: "*.bed" + - - vcf_output: + type: file + description: VCF output file + pattern: "*.vcf.gz" + - - snf_output: + type: file + description: SNF output file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz.tbi": + type: file + description: Compressed VCF file index + pattern: "*.tbi" - snf: - type: file - description: SNF file - pattern: "*.snf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.snf": + type: file + description: SNF file + pattern: "*.snf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-hakkaart" - "@yuukiiwa" maintainers: - "@christopher-hakkaart" - "@yuukiiwa" + - "@fellen31" diff --git a/modules/nf-core/sniffles/sniffles.diff b/modules/nf-core/sniffles/sniffles.diff index b36fb319..30d9c425 100644 --- a/modules/nf-core/sniffles/sniffles.diff +++ b/modules/nf-core/sniffles/sniffles.diff @@ -1,110 +1,67 @@ Changes in module 'nf-core/sniffles' ---- modules/nf-core/sniffles/meta.yml -+++ modules/nf-core/sniffles/meta.yml -@@ -17,10 +17,10 @@ - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] -- - bam: -+ - input: - type: file -- description: BAM file -- pattern: "*.bam" -+ description: BAM or SNF file -+ pattern: "*.{bam, snf}" - - bai: - type: file - description: Index of BAM file -@@ -34,6 +34,15 @@ - type: file - description: | - Reference database in FASTA format -+ - meta3: -+ type: map -+ description: | -+ Groovy Map containing tandem repeat file information -+ e.g. [ id:'tandem_repeats' ] -+ - tandem_file: -+ type: file -+ description: | -+ Tandem repeats file in BED format - output: - - meta: - type: map -@@ -46,8 +55,8 @@ - pattern: "*.vcf.gz" - - snf: - type: file -- description: Compressed SNF file -- pattern: "*.snf.gz" -+ description: SNF file -+ pattern: "*.snf" - - versions: - type: file - description: File containing software versions - +'modules/nf-core/sniffles/meta.yml' is unchanged +Changes in 'sniffles/main.nf': --- modules/nf-core/sniffles/main.nf +++ modules/nf-core/sniffles/main.nf -@@ -8,14 +8,17 @@ - 'biocontainers/sniffles:2.0.7--pyhdfd78af_0' }" +@@ -4,16 +4,15 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/sniffles:2.4--pyhdfd78af_0' : +- 'biocontainers/sniffles:2.4--pyhdfd78af_0' }" ++ 'https://depot.galaxyproject.org/singularity/sniffles:2.0.7--pyhdfd78af_0' : ++ 'biocontainers/sniffles:2.0.7--pyhdfd78af_0' }" input: -- tuple val(meta), path(bam), path(bai) +- tuple val(meta), path(input), path(index) + tuple val(meta), path(input), path(bai) tuple val(meta2), path(fasta) + tuple val(meta3), path(tandem_file) + val(vcf_output) + val(snf_output) - -+ tuple val(meta3), path(tandem_file) -+ val(vcf_output) -+ val(snf_output) output: -- tuple val(meta), path("*.vcf"), emit: vcf -- tuple val(meta), path("*.snf"), emit: snf -- path "versions.yml" , emit: versions -+ tuple val(meta), path("*.vcf.gz") , emit: vcf, optional: true -+ tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true -+ tuple val(meta), path("*.snf") , emit: snf, optional: true -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -23,14 +26,33 @@ - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" -+ def reference = fasta ? "--reference ${fasta}" : "" -+ def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : '' -+ def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": '' -+ def snf = snf_output ? "--snf ${prefix}.snf": '' + tuple val(meta), path("*.vcf.gz") , emit: vcf, optional: true +@@ -31,7 +30,7 @@ + def tandem_repeats = tandem_file ? "--tandem-repeats ${tandem_file}" : '' + def vcf = vcf_output ? "--vcf ${prefix}.vcf.gz": '' + def snf = snf_output ? "--snf ${prefix}.snf": '' +- + """ sniffles \\ -- --input $bam \\ -- --vcf ${prefix}.vcf \\ -- --snf ${prefix}.snf \\ -- --reference $fasta \\ -+ --input $input \\ -+ $reference \\ - -t $task.cpus \\ -+ $tandem_repeats \\ -+ $vcf \\ -+ $snf \\ + --input $input \\ +@@ -41,21 +40,18 @@ + $vcf \\ + $snf \\ $args +- + -+ cat <<-END_VERSIONS > versions.yml -+ "${task.process}": -+ sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') -+ END_VERSIONS -+ """ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') + END_VERSIONS + """ +- + -+ stub: -+ def prefix = task.ext.prefix ?: "${meta.id}" -+ """ + stub: + def prefix = task.ext.prefix ?: "${meta.id}" +- def vcf = vcf_output ? "echo \"\" | gzip > ${prefix}.vcf.gz; touch ${prefix}.vcf.gz.tbi": '' +- def snf = snf_output ? "touch ${prefix}.snf": '' +- + """ +- ${vcf} +- ${snf} + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.snf -+ + cat <<-END_VERSIONS > versions.yml "${task.process}": - sniffles: \$(sniffles --help 2>&1 | grep Version |sed 's/^.*Version //') +'modules/nf-core/sniffles/environment.yml' is unchanged +'modules/nf-core/sniffles/tests/tags.yml' is unchanged +'modules/nf-core/sniffles/tests/main.nf.test.snap' is unchanged +'modules/nf-core/sniffles/tests/nextflow.config' is unchanged +'modules/nf-core/sniffles/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/sniffles/tests/main.nf.test b/modules/nf-core/sniffles/tests/main.nf.test new file mode 100644 index 00000000..9560b02d --- /dev/null +++ b/modules/nf-core/sniffles/tests/main.nf.test @@ -0,0 +1,286 @@ +nextflow_process { + + name "Test Process SNIFFLES" + script "../main.nf" + process "SNIFFLES" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "sniffles" + + test("homo_sapiens - [bam, bai], fasta, [], true, false") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = true + input[4] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.tbi.get(0).get(1)).name, + path(process.out.vcf.get(0).get(1)).linesGzip[0..1], + path(process.out.vcf.get(0).get(1)).linesGzip[4..62], + ).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, [], false, true") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = false + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.snf.get(0).get(1)).name, + ).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, [], true, true") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = true + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.snf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name, + path(process.out.vcf.get(0).get(1)).linesGzip[0..1], + path(process.out.vcf.get(0).get(1)).linesGzip[4..62], + ).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, bed, true, true") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[3] = true + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.snf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name, + path(process.out.vcf.get(0).get(1)).linesGzip[0..1], + path(process.out.vcf.get(0).get(1)).linesGzip[4..62], + ).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, [], true, false -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = true + input[4] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, [], false, true -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = false + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, [], true, true -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[],[]] + input[3] = true + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [bam, bai], fasta, bed, true, true -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[3] = true + input[4] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/sniffles/tests/main.nf.test.snap b/modules/nf-core/sniffles/tests/main.nf.test.snap new file mode 100644 index 00000000..cb690bac --- /dev/null +++ b/modules/nf-core/sniffles/tests/main.nf.test.snap @@ -0,0 +1,481 @@ +{ + 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TAAATTCTTAAATCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCGTCTCAGTATTTCTATTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCAATTCCAGGTAAACTTTGGCCTTTTATGAATTCTCCTGATCAGGCCAAACCTCAACCAAGTCCCTTCTTGATCTTCTCCTTCACCTCCTTCCCTCATTCACCCAACAATTAGCCTCCAGTCCACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAAGCCTCAGCTAAAGTTTACAATCCTACCTTTTCTACTGCCTTGAAATGCCCTAAGGTTCAGGGGCTTCATGGTTGCTGCTTCATGGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCCGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTCTACAGCTCTGCTGTCCCATTAACAGCACCTTTGGGGCCCCAGGGTTCCAGATTGGAAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCTTTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTCTACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAGAGGATCTTTAGCCTGCGGCGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAAGGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGATCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAATAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGAGGAAAGGATGGAAACTACTACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCTTCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGTTTTTGTAGATTGAAGTCTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCCAGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGAAATCCTTCCACCTCAGCCCCCCAAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGTTAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAAGTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGTATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGGCCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCAAATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCATCTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGCTATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGAAGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGGCCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCCCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGAAAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACAGCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAATATCTGAGACCTAGCATGCTAGGAGACCTTTATCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAAATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGATGTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCA\t44\tCOV_CHANGE_INS\tPRECISE;SVTYPE=INS;SVLEN=7407;END=0;SUPPORT=3;COVERAGE=0,0,0,0,8;STRAND=+-;STDEV_LEN=16.000;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t./.:0:0:0", 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TAAATTCTTAAATCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCGTCTCAGTATTTCTATTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCAATTCCAGGTAAACTTTGGCCTTTTATGAATTCTCCTGATCAGGCCAAACCTCAACCAAGTCCCTTCTTGATCTTCTCCTTCACCTCCTTCCCTCATTCACCCAACAATTAGCCTCCAGTCCACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAAGCCTCAGCTAAAGTTTACAATCCTACCTTTTCTACTGCCTTGAAATGCCCTAAGGTTCAGGGGCTTCATGGTTGCTGCTTCATGGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCCGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTCTACAGCTCTGCTGTCCCATTAACAGCACCTTTGGGGCCCCAGGGTTCCAGATTGGAAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCTTTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTCTACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAGAGGATCTTTAGCCTGCGGCGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAAGGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGATCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAATAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGAGGAAAGGATGGAAACTACTACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCTTCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGTTTTTGTAGATTGAAGTCTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCCAGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGAAATCCTTCCACCTCAGCCCCCCAAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGTTAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAAGTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGTATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGGCCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCAAATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCATCTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGCTATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGAAGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGGCCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCGGATCCCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCATTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAAGAAAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACAGCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAATATCTGAGACCTAGCATGCTAGGAGACCTTTATCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAAATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGATGTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCA\t44\tCOV_CHANGE_INS\tPRECISE;SVTYPE=INS;SVLEN=7407;END=0;SUPPORT=3;COVERAGE=0,0,0,0,8;STRAND=+-;STDEV_LEN=16.000;STDEV_POS=0.000;SUPPORT_LONG=0\tGT:GQ:DR:DV\t./.:0:0:0", 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CCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGACTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCGGTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGATCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAACTTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCCGCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTTCGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGATTCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGAGCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGGAAGCGCAGGAGCCGGCTGGGGGAGGGGGCGCCCTAGAGAAGCGGCTAGAAAGCTGAGACGGGGAACTGAGGTCATCCTGGGGGGGACAAGACAATGAGAGCCGGGCGCCTTGGGGGCGGCGCGGGAGCCTCCGCAGGACCAGGCGGGCGCCCCCTTTACCTGCGGCTCCGGCGCCTCGGCCGTTTCCTCGCGCGGCGGCGGCCGGGACTGAGCTGACACCACTCAGCCGGCGGGGTTTGAATGAGGAGGAGCGGGCGCGGAGGGGAGGGGGCGGGGAGGGAGGGAGGGAGGCGTCGCGGAGTTTCTCTCGGCCTTTTGTGCCATCCGCCGAGGCGCCTTGAGTATAAATCCAGATAGTGCAGTTTTTGTTGTGCTTGTGCTGATCAACTTTATGGTGTGATTAAATACGATTTTTTTTATTACGCTCTTGAAATTGTACTCTTGAGGTTGCAGAATGGCAATTAGATGGCAGTCGCTGATAGCCATGTAGAAGTTTTGATGAACATGCAAGTTAATTTTAATTTCTGATCAGTTACGGTTAGTGACTGTGGCCAAACATGTGCGTACTGATTCTACATGTGCTAATTCCGTGACGTTTATTCACCAGCTATGTGTCCCGTGCCTAATCCTGTGTCAGGCACCTTGTTCCAGGCATTGGGGGCAGCAGTGGACAAGGCAACAGAGTCTCCATCCTGAGGTGTTACTTTTAGAAAAAGATAGTTACAAGCAAATAAACAGGATGGTTTTAGATCTGGACAGAGGTTTTCAGAGGAAGTCATCCTTGAGCTGTCACAATGCTTTGGGGAGGGGTGTGCTGGGTAATCAGGGATGGCACATTTGGGGTGCCTAAGGATTGCTGTGGCCCTGGGAGCCTAGGACAGTTGGTCACAATTGACTTATTAGAGTCAGTCTCAGAAGCTTTCCTGGAAGTAGAATTGCTGCTGTTTTGCCAGGAGGGTTTCCTTCCCCATCTGACCACACAAGAAGACCCCTGCCCACAAATGCCTACCACTCCCAGGTCTCCCAGGCTGTTCACCCTCCCAGGCAAAGTGGAAGCTTCCTCTGTCCTAAGATCGTTTCCCACTGAACCTCCTTCATTTTCCTTCACTGCAGAGAAATAATCCTACAAGGTCTTGTGTGGAGAGTGATGGTACCTTCTTTAACCCAGATAATTGAGAATTGGAACCAAAACATCTGTGTATTAATAAATATTTTCAGTAACTAGGTTATGCTATTTCCCTGAGTGGGAAATAACACTCCATCATGTTTCTTTTTTTGGGGGGCAAGGGGGAGTCAAAGTTGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCGTGACTTGCACATATACATCCAGATGGCCTGAAGTAATTGAAGATCCACAGAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAATCTCCCCCACCCTTAAGAAGGTTCTTTGGAGTCTCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGACTGTAATTTTCCATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTCCCTTCACTTGACTCTCTTTTCAGACTCAGCCCACCTGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACGAAGCCTGTTTGGTGGTCTCTTCACACGGATGCGCATGAAATTTGGTGCCGTGACTTGGATCGGGGGACCTCCCTTAGGAGATCAATCCCCTGTCCTCCTGCTCTTTGCTCCGTGAGAAAGATCCACCTACGACCTCAGGTCCTCAGACCGACCAGCCCAAGAAACATCTCACCAATTTCAAATCTGGTAAGCGGCCTCTTTTTACTCTCTTCTCCATTCCTCCTCCTTCTCCCTTAGCTTCTCCAACCTCCCTCACTATCCCTCAACCTCTTTCTCCTTTCAATCTTGGCGCCACACTTCA\t7\tPASS\tPRECISE;SVTYPE=INS;SVLEN=7453;END=10115;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.300;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/1:10:7:3", + "chr22\t10126\tSniffles2.INS.1S0\tA\tACCGCTTTTCTGGGGCAGGGGCAAGTACCCCTCAACCCCTTCCCCTTCACACTTAGTGGCAAGTCCCGCTTTCCTGGGCAGGGGCAAGTACCCCTCAACGCCTTCTCCTTCACCCTTAGTGGCAAGTCCCGCTTTTCTAGGGGGGCAAGAACCCCCAAACCCCTTCCATCTGTGTCTCTACGCTCTCTTCTGTGGGTTTGCTTCCTTCACTATGGAACCTTCCACCCTCCATTCCTCCTTCTTCTCCCTTAGCCTGTGTGCTCAAAAAGTTAAAACCTCTTCAACTCACACCTGACCTAAAACCTAAATGCCTTATTTTCTTCTGCAACACCGCATATCTTGCTTGGCCCCAATACAAACTTGACAATGTCTCTAAATGGCCGGAAAATGGCACTTTGATTTCCCCACTGACAAACACCTAAATAATTTTTGTCGAAAAATGGGCAAATGGTCTGAGGTGCCTTACGTCCAGGCATTTTTCACACTTCGTTCCCTCCCTAGTCTCTGTTCCCAATGCGATTCCTCCCAGATCCTCCTCCTTTCCTCTCCTGTCCCCTCGGTCCCAACCCCAAGCGTCGCTGAGTCTTCCCAGTCTTCCTTTTCTACAGACCCATCTGACCTTTCCCCTCCTCCCCAAGCTGCTTGTCGCCAGACCGAGCTAAGTCCCAAGTACCTCCCTCAACTCTCCACTCCTCCACCCTATAATCCTTCTATCACCTCCCCTCCTCACACCTGGTCCGGCTTACAGTTTAGTTCCGCGACTAGCGCTTCCCCACCTGCCCAACAATTTCCTCTTAGAGAAAGTGGCTGGAGCTGAAGGCATAGTCAAGGGACATGTACTTTTTTCTCTATCAGACCTCTCTCAGATCAGTCAATGTTTAGGCTCTTTCTCATCAGACCCCACTAAATATATACAGGAATTCCAATATCTAACTCTGTCCTACAACTTAACCTGGAGTGACTTAAATGTCATCCTGACTTCTACTCTCTCCCCAATATGAACGGGAAAGTTTTTTCTCTAGCCCAATCTCGTGCTGATAACCGCCGGCTTCATGAGCCAGACCTCCAGGAAGGCATTAGAGCAGTTCCCCGAGAGGATCCCCAATGGAACTATCAGGCAGATTCCCCAGGTACAGCTAGGCGAGATTACATGGTTTCCTGCCTAGTTGAAGGGCTTAAAAAAGCAGCTTACAAAGCTGTTAATTATGACAAGCTTAAAGAAACTACCCGAGGTAAAGACGAAAACCCAGCCCAGGTCATGGCCCACTTAGCAGCAACCATTAGATGCTATACTGCCCTAGACCCAGAGGGGCCAGAAGGCCGCCTTATTCTTAATATGCATTTTTATCACCCAATCCACTCCTGACATTAGGAAAAAACTTCAAAAATTAGAATCTGGCCTTCAAACCCAGCAGGAATTAATCAACCTTGCCTTCAAGGTGTACAATAATAGAGAGGAAGCAGCCAGACGGCAACGCATTTCGAGTTACAATTACTTGCCTCTGCTGTGAGACAAAACCCAGCCACACCTCCTGCATACAGGAACTTCAAAATGCCTAAGCCGCAGCAATCAGACACTCCTACAAGACTTCATCAGGATCTTGCTTCAAGTGCCAGAAATCTGGCCACTGGGCCAAGGAATGCCCACAGCCCAGGATTCCTCCCAAGCCATGTCCCATCTGTGCAGGCACCCACTGGAAATCAGACTGCCCAGCTCGCCCGACAGCCACTCCTGGAGCCCCTAAAGCTCTAGCCCAAGGCTCTCTGACTCCTTCCCAGATCTATTCGGCTTAGCGACTGAAGATTGACGCTGCCCGATCGCCTCGGAAGTCCCCTGGACCATCACAGAAGCCGAGCTTCGGGTAACTCTCACAGTGGAGGGTAAGTCCATCCCCTGTTTAATCGATACGGGGGCTACCCACTCCACGTTGCCTTCTTTTCAAGGGCCTGTTTCCCTTGCCCCCATAACTGTTGTGGGTATTGACGGCCAAGCTTCAAAACCCCTGAAAACTCCCCCACTCTGGTGCCAACTTGGACAACACTCTTTTATGCACTCTTTTTTAGTTATCCCCACCTGCCCACTTCCCTTATTAGGCCGAAATATTTTAACCAAATTATCTGCTTCCCTGACTATTCCTGGAGTACAGCTACATCTCATTGCTGCCCTTCTTCCCAATCCAAAGCCTCCTTTGTGTCCTCTAACATCCCCACAATATCACCCCTTACCACAAGACCTCCCTTCAGCTTAATCTCTCCCACTCTAGGTTCCCACGCCGCCCCTAATCCCACTTGAAGCAGCCCTGAGAAACATCGTCCATTCTCTCTCCATACCACCCCCCAAAAATTTTCGCCGCTCCAACACTTCAACACTATTTTGTTTTATTTGTCTTATTAATATCAGAAGGCAGGAATGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCCTGTGACTTGCACGTATACATCCAGATGGCCTGAAGTAACTGAAGATCCACAAAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAGACTCCCTCCCCCCACCCTTAAGAAGGTTCTTTGTAATTCTCCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGATTGTAATTTTTTATTACCTTCCCAAATCCTATAAAACAGCCCCACCCCTATCTTCCTTCACTGAACTCTCTTTTCGGACTCAGCCCACCGGCACCCAGGTGAAATAAACAGCTTTATTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGTATGAAAAAAGTCTCGCCCTGTTGCCCAGGCTGGAATGCAGTGGCACGATCTTGGCTCACTGCTACCTCCACTTCCTGGGTTCAAGTGATTCCCAAGTAGCTGGGATTACAGGTGTGTATTACCATGCCCAGCTAATTTTTGTATTTTTAGCAGATAAGGGGTTTCACCATGTTGGCCAGGCTGGTCTCCAACTCCTGGCCTCAAGTGATCCACCCACTTCGGCTACCCAAAGCATTGGGAGTACAGGGGTGAGCCACTATGCCCAGCCTCACATCATATTTCTAATCCCGAGACTGTAGAGCTGGTGTCTCTTTTTGGAAAGGATGTCAGTAGAGAAAATGGAGTTCCCCAAAATTACAGTTTCACATATTAGTAAAGTTTCTAAAATACAGTAATAATGTTGAGAGCTGACATAGGGACTAACTTAGTTTTTTTTTTTTTTTAGATTGTCACCTAACTTTGATTTTGCTAAATAAGGACATTAAAAGAAAACCAAAAAAGTCCACTATTGGCTATTGCCACTATTTGATTTTTTAAAAAATAAGCGTATTTTAGCATCTAAAAGTAGGAAGGACCTCAAATAAATGAGTCTTTGTTCTTGGCCAGGGAAACAGCGTTGTCAGCATTTGATAACTGTTTTTCTAGGGTATGTGCTGTTATTCAGTTAAAACCTTGCCTGGGGATGTTAGCATTGGTAAATACTTGTTGAATAAGCAAATGAAACTTAAGCTTCTATGTATAGAAACCTAAGTCACTTCACATTCTGATTAGCAGAGTAATTGAATATTCTTTTCAGTGTGTAGATCTATACCCAGAACCACAGAATATCGGAACTGTAAAAACCAACTGCATTAAATAGATGTGGTATGTGGCAGTGTACCAAGGTTGTGACTAGAACTCCGGTCTTGGAGTGTTCTATTATATCACACCAAGCTGGTCACCAGCCCATGTGTTGATCCTCCATTGTGATAGCAACAAAGAAAAGACTTCAGGACATTCTTTCCTTTACCCTAATCCTTCATCTTCAGTCTTATTTAGAAAAGCTTAATGTTAAAGATCTAGTTTATTCAAAACTAAAGATAAGGAGTATGAGAATTTCTATTTCGGAGTGTAAAGGAGGAGATGTTTCCTTGGCTTCTCTGAGCCTACAGGCCTTCCTTGCTCTTTAAGGAAGTAGAGAGAGAGAGGAAAGTAAAGTATGCTTTTGTTTTTTAAGGTTACTTTGCTGGGAGTAGTTTGCATGCCATTTGGTTTTCTTGGGTGGAATTAACTGACTTAAGTTTTAAGTAGTTGGGACTATTTAGAAACAATGCCTATCCAATGTTTGCCATAAAGGCAGAGGGTATTGGCTTTAGAAGTTAATTCTTCTCCAGGAGTGAAAATGAGCTGCTAAACCAGAAGCAGCAGAGCTAAAGAAAGTAATTTTCCACCTGGCCAGTGCATGATGTGAAAGGTAGACTAAAAGAATGAGAGGACCCATTTTCTGATGAAAGACTAAGCCATGTTGAAACAGCCCTGTTGAGGATTTTATTTTAAATCTATACATTCACAAAGGAGCTTTGTGTATGTCTTTCCCTATTTGTTGTTTGGACTAAGGGAGCCCCACCCAGTGCTTGTTCAGTAAGTTGTTGAAAGAAATCTGGATTTGAACAGTGGATTGAGGTTTCGAATATCCAGTGAACCAAAATATATCAGGGTTCCCCTGGCCAAGATGAGTGACCATTCTGAGGTGTTACGTATTTCTTGAATGGGGATTTTAGGAAAAGTTTCTGTATTTCTGTGCTCATTTTGTTGACCTCTGTATGTGCAAAATCTCTAAGGGGGTGTTTGGGCACTTAGATTTCTTGGATGCAGATTTGTTTGTATATGAAACAAATTTTAAATTGTTTCGTATACACTGGATTTAAAATAGTTTAGTTTACTAAAGTGTTTTAATGTTTTCATCTTAATTTTCAGTTCTTATAGTCTTTAGATTTAGGGAGGCTGTTGATGGCATCCACATATGCATTTTAATGTCATTTAAAATGTATTCTGCTGAATTTAACAATTTCTGACCTAAAACTTGACATTTTAATATTTAAGTCGGTAAAGCGCTGATTTAAACTGGATTTTAACTGGATGAAATTCTGATTTAATGAGTGTACTGACTGGATAAAATGCCAATGATTTAATTAACAAGCACGTTTACAGCATGCCCTATATATTAGTTAAAAGTGAAGCAATTGAATTAGGTACCATTTCAAAATGGTTGCTGTACCCACTCACCCTCTCTATCCTCCAATTAGGGTATATTTTGAAATGATTGCTTTTCCCTTTTCCTTGTGTAAAGAGCCTGAGGAAATTTTCTTCGGCCTTCATCATGAGAACCTGGTGGGGTTTCTGGAAGTAAAATTCATGAAAGTATAAGGGGCCCCCAAGACGGGACTCCAACAAGTTTTTAACTCTCAAGCTAGTCCACACTCAGCCACCAGTAAATTTATTGATTACCATTGAAGTGTTCCTACCAATTAC\t9\tPASS\tPRECISE;SVTYPE=INS;SVLEN=5362;END=10126;SUPPORT=1;COVERAGE=10,10,10,29,10;STRAND=-;AF=0.200;STDEV_LEN=0;STDEV_POS=0;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:2:8:2", + "chr22\t13000\tSniffles2.INS.3S0\tT\tTGATAATCAAGAGAACGTCTCAGCACCGCGCCTGAGCGCTTAGTAGGTAGTGATCAAGAGAGAAGACCTC\t36\tGT\tIMPRECISE;SVTYPE=INS;SVLEN=69;END=13000;SUPPORT=2;COVERAGE=11,13,13,16,51;STRAND=+-;AF=0.154;STDEV_LEN=6.364;STDEV_POS=37.477;SUPPORT_LONG=0\tGT:GQ:DR:DV\t0/0:10:11:2" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-30T13:26:44.362217872" + } +} \ No newline at end of file diff --git a/modules/nf-core/sniffles/tests/nextflow.config b/modules/nf-core/sniffles/tests/nextflow.config new file mode 100644 index 00000000..06e38362 --- /dev/null +++ b/modules/nf-core/sniffles/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'SNIFFLES' { + ext.args = '--minsupport 1 --no-qc --mapq 0' + } +} diff --git a/modules/nf-core/sniffles/tests/tags.yml b/modules/nf-core/sniffles/tests/tags.yml new file mode 100644 index 00000000..7010d53c --- /dev/null +++ b/modules/nf-core/sniffles/tests/tags.yml @@ -0,0 +1,2 @@ +sniffles: + - "modules/nf-core/sniffles/**" diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index fe32ebda..757967b2 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -1,7 +1,5 @@ -name: somalier_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.18 diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index aabaf5d6..25621667 100644 --- a/modules/nf-core/somalier/extract/meta.yml +++ b/modules/nf-core/somalier/extract/meta.yml @@ -1,5 +1,6 @@ name: "somalier_extract" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,65 +15,69 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file - - input_index: - type: file - description: index file of the input data, e.g., bam.bai, cram.crai - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fna,fas,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing sites information - e.g. [ id:'hg38' ] - - sites: - type: file - description: sites file in VCF format which can be taken from https://github.com/brentp/somalier - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file + - input_index: + type: file + description: index file of the input data, e.g., bam.bai, cram.crai + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fna,fas,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fai: + type: file + description: FASTA index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing sites information + e.g. [ id:'hg38' ] + - sites: + type: file + description: sites file in VCF format which can be taken from https://github.com/brentp/somalier + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - extract: - type: file - description: binary output file based on extracted sites - pattern: "*.{somalier}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somalier": + type: file + description: binary output file based on extracted sites + pattern: "*.{somalier}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/somalier/extract/somalier-extract.diff b/modules/nf-core/somalier/extract/somalier-extract.diff index 59f472ab..b1118b5e 100644 --- a/modules/nf-core/somalier/extract/somalier-extract.diff +++ b/modules/nf-core/somalier/extract/somalier-extract.diff @@ -1,4 +1,6 @@ Changes in module 'nf-core/somalier/extract' +'modules/nf-core/somalier/extract/meta.yml' is unchanged +Changes in 'somalier/extract/main.nf': --- modules/nf-core/somalier/extract/main.nf +++ modules/nf-core/somalier/extract/main.nf @@ -5,8 +5,8 @@ @@ -13,13 +15,17 @@ Changes in module 'nf-core/somalier/extract' input: tuple val(meta), path(input), path(input_index) +Changes in 'somalier/extract/environment.yml': --- modules/nf-core/somalier/extract/environment.yml +++ modules/nf-core/somalier/extract/environment.yml -@@ -4,4 +4,4 @@ +@@ -2,4 +2,4 @@ + - conda-forge - bioconda - - defaults dependencies: - - bioconda::somalier=0.2.19 + - bioconda::somalier=0.2.18 +'modules/nf-core/somalier/extract/tests/tags.yml' is unchanged +'modules/nf-core/somalier/extract/tests/main.nf.test.snap' is unchanged +'modules/nf-core/somalier/extract/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml index 3a730471..757967b2 100644 --- a/modules/nf-core/somalier/relate/environment.yml +++ b/modules/nf-core/somalier/relate/environment.yml @@ -1,7 +1,5 @@ -name: somalier_relate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.18 diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml index 42638f4f..0da72821 100644 --- a/modules/nf-core/somalier/relate/meta.yml +++ b/modules/nf-core/somalier/relate/meta.yml @@ -1,5 +1,6 @@ name: "somalier_relate" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,47 +15,67 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - extract: - type: file - description: extract file(s) from Somalier extract - pattern: "*.somalier" - - ped: - type: file - description: optional path to a ped or fam file indicating the expected relationships among samples - pattern: "*.{ped,fam}" - - sample_groups: - type: file - description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line - pattern: "*.{txt,csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - extract: + type: file + description: extract file(s) from Somalier extract + pattern: "*.somalier" + - ped: + type: file + description: optional path to a ped or fam file indicating the expected relationships + among samples + pattern: "*.{ped,fam}" + - - sample_groups: + type: file + description: optional path to expected groups of samples such as tumor normal + pairs specified as comma-separated groups per line + pattern: "*.{txt,csv}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: html file - pattern: "*.html" + - meta: + type: file + description: html file + pattern: "*.html" + - "*.html": + type: file + description: html file + pattern: "*.html" - pairs_tsv: - type: file - description: tsv file with output stats for pairs of samples - pattern: "*.pairs.tsv" + - meta: + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" + - "*.pairs.tsv": + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" - samples_tsv: - type: file - description: tsv file with sample-level information - pattern: "*.samples.tsv" + - meta: + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - "*.samples.tsv": + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff index f583d612..7dd8b76c 100644 --- a/modules/nf-core/somalier/relate/somalier-relate.diff +++ b/modules/nf-core/somalier/relate/somalier-relate.diff @@ -1,4 +1,6 @@ Changes in module 'nf-core/somalier/relate' +'modules/nf-core/somalier/relate/meta.yml' is unchanged +Changes in 'somalier/relate/main.nf': --- modules/nf-core/somalier/relate/main.nf +++ modules/nf-core/somalier/relate/main.nf @@ -5,8 +5,8 @@ @@ -13,13 +15,17 @@ Changes in module 'nf-core/somalier/relate' input: tuple val(meta), path(extract), path(ped) +Changes in 'somalier/relate/environment.yml': --- modules/nf-core/somalier/relate/environment.yml +++ modules/nf-core/somalier/relate/environment.yml -@@ -4,4 +4,4 @@ +@@ -2,4 +2,4 @@ + - conda-forge - bioconda - - defaults dependencies: - - bioconda::somalier=0.2.19 + - bioconda::somalier=0.2.18 +'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/splitubam/environment.yml b/modules/nf-core/splitubam/environment.yml index ef128202..382f9112 100644 --- a/modules/nf-core/splitubam/environment.yml +++ b/modules/nf-core/splitubam/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "splitubam" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::splitubam=0.1.1" diff --git a/modules/nf-core/splitubam/meta.yml b/modules/nf-core/splitubam/meta.yml index 3d11eaae..64691357 100644 --- a/modules/nf-core/splitubam/meta.yml +++ b/modules/nf-core/splitubam/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "splitubam" description: split one ubam into multiple, per line, fast @@ -13,33 +12,34 @@ tools: documentation: "https://github.com/fellen31/splitubam" tool_dev_url: "https://github.com/fellen31/splitubam" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - bam: - type: file - description: (u)BAM file - pattern: "*.{bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: (u)BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Split (u)BAM file - pattern: "*.{bam}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Split (u)BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml index 530ce375..c476e2b3 100644 --- a/modules/nf-core/stranger/environment.yml +++ b/modules/nf-core/stranger/environment.yml @@ -1,7 +1,5 @@ -name: stranger channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::stranger=0.9.1 + - bioconda::stranger=0.9.2 diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 923483f4..bc31e703 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -4,8 +4,8 @@ process STRANGER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stranger:0.9.1--pyh7e72e81_0': - 'biocontainers/stranger:0.9.1--pyh7e72e81_0' }" + 'https://depot.galaxyproject.org/singularity/stranger:0.9.2--pyh7e72e81_0': + 'biocontainers/stranger:0.9.2--pyh7e72e81_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml index 5e0bc0bb..a5486dbd 100644 --- a/modules/nf-core/stranger/meta.yml +++ b/modules/nf-core/stranger/meta.yml @@ -1,5 +1,6 @@ name: stranger -description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes. +description: Annotates output files from ExpansionHunter with the pathologic implications + of the repeat sizes. keywords: - STR - repeat_expansions @@ -13,39 +14,42 @@ tools: tool_dev_url: https://github.com/moonso/stranger doi: "10.5281/zenodo.4548873" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF with repeat expansions - pattern: "*.{vcf.gz,vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - variant_catalog: - type: file - description: json file with repeat expansion sites to genotype - pattern: "*.{json}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF with repeat expansions + pattern: "*.{vcf.gz,vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - variant_catalog: + type: file + description: json file with repeat expansion sites to genotype + pattern: "*.{json}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ljmesi" maintainers: diff --git a/modules/nf-core/stranger/tests/main.nf.test b/modules/nf-core/stranger/tests/main.nf.test index 13c61f43..3c12a2c5 100644 --- a/modules/nf-core/stranger/tests/main.nf.test +++ b/modules/nf-core/stranger/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { script "../../expansionhunter/main.nf" process { """ - input[0] = [ + input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) diff --git a/modules/nf-core/stranger/tests/main.nf.test.snap b/modules/nf-core/stranger/tests/main.nf.test.snap index 3faa4e58..b0ce7380 100644 --- a/modules/nf-core/stranger/tests/main.nf.test.snap +++ b/modules/nf-core/stranger/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c" + "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb" ], "vcf": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c" + "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T08:09:27.725425094" + "timestamp": "2024-11-04T10:27:41.164430492" }, "homo_sapiens - vcf, repeat_catalogue": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c" + "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb" ], "vcf": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,68446c9e91e20825f7430db64e85aa7c" + "versions.yml:md5,a3f4f3b2391e96e77caa158199436fcb" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T08:09:14.472394433" + "timestamp": "2024-11-04T10:27:31.05008915" } } \ No newline at end of file diff --git a/modules/nf-core/stranger/tests/nextflow.config b/modules/nf-core/stranger/tests/nextflow.config index 98459330..0ddc8bbd 100644 --- a/modules/nf-core/stranger/tests/nextflow.config +++ b/modules/nf-core/stranger/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: 'STRANGER' { - ext.prefix = "stranger" - } - } + withName: 'STRANGER' { + ext.prefix = "stranger" + } +} diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 96d21eba..24c5effd 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -1,6 +1,6 @@ process SVDB_MERGE { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd:b3615e06ef17566f2988a215ce9e10808c1d08bf-0': diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml index cd35cf48..2af55220 100644 --- a/modules/nf-core/svdb/query/environment.yml +++ b/modules/nf-core/svdb/query/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::svdb=2.8.1 + - bioconda::svdb=2.8.2 diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index d516d382..4ceb477a 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -4,8 +4,8 @@ process SVDB_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/svdb:2.8.1--py39h5371cbf_0': - 'biocontainers/svdb:2.8.1--py39h5371cbf_0' }" + 'https://depot.galaxyproject.org/singularity/svdb:2.8.2--py39h5371cbf_0': + 'biocontainers/svdb:2.8.2--py39h5371cbf_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap index 22021d0a..65f2fcfa 100644 --- a/modules/nf-core/svdb/query/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/query/tests/main.nf.test.snap @@ -4,27 +4,10 @@ "test_query.vcf", "versions.yml" ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, "timestamp": "2023-11-22T14:56:08.90223505" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,e10873514a6dfc4ff377d645e7b3c9f5" - ] - ], - "timestamp": "2023-11-22T14:36:48.543666873" - }, - "vcf": { - "content": [ - [ - [ - { - "id": "test" - }, - "test_query.vcf:md5,a29542606323b2430ec52ffb5c4c7f5e" - ] - ] - ], - "timestamp": "2023-11-22T14:36:48.523155905" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 56cc0fb1..017c259d 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,8 +1,7 @@ -name: tabix_bgzip channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index 621d49ea..131e92cf 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -13,33 +13,42 @@ tools: documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: file to compress or to decompress + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: file to compress or to decompress output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output compressed/decompressed file - pattern: "*." + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: Output compressed/decompressed file + pattern: "*." - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}.gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index b9644de9..017c259d 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,8 +1,7 @@ -name: tabix_bgziptabix channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 05041f49..22f37a77 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" + def args2 = task.ext.args2 ?: '' + def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi" """ echo "" | gzip > ${prefix}.${input.getExtension()}.gz - touch ${prefix}.${input.getExtension()}.gz.tbi - touch ${prefix}.${input.getExtension()}.gz.csi + touch ${prefix}.${input.getExtension()}.gz.${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 438aba4d..806fbc12 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -13,38 +13,50 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file - pattern: "*.{bed,gff,sam,vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Sorted tab-delimited genome file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gz: - type: file - description: Output compressed file - pattern: "*.{gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{gz.tbi}" - - csi: - type: file - description: tabix alternate index file - pattern: "*.{gz.csi}" + - gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.tbi": + type: file + description: tabix index file + pattern: "*.tbi" + - gz_csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.csi": + type: file + description: csi index file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@DLBPointon" diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 1a84d74f..4d4130dc 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -91,4 +91,33 @@ nextflow_process { } + test("sarscov2_bed_tbi_stub") { + config "./tabix_tbi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_stub") + } + ) + } + + } + } diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap index c166ea72..fb87799b 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -91,6 +91,47 @@ }, "timestamp": "2024-02-19T14:51:00.548801" }, + "sarscov2_bed_tbi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.533169949" + }, "csi_stub": { "content": [ "test.bed.gz" @@ -101,6 +142,16 @@ }, "timestamp": "2024-02-19T14:51:09.218454" }, + "tbi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.550930179" + }, "tbi_test": { "content": [ "tbi_test.bed.gz" @@ -115,13 +166,7 @@ "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ [ @@ -145,13 +190,7 @@ ] ], "gz_tbi": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" @@ -159,9 +198,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-19T11:29:45.105209991" + "timestamp": "2024-09-25T14:44:19.786135972" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 4d1f9dd4..017c259d 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,9 +1,6 @@ -name: tabix_tabix - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index ae5b4f43..7864832d 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -11,34 +11,43 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file compressed with bgzip - pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" - csi: - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/subworkflows/local/annotate_svs/tests/main.nf.test.snap b/subworkflows/local/annotate_svs/tests/main.nf.test.snap index c56c9824..c39dd47a 100644 --- a/subworkflows/local/annotate_svs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_svs/tests/main.nf.test.snap @@ -4,21 +4,21 @@ [ "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed", - "versions.yml:md5,cb83982d3231b281882f4ddc478d93ae" + "versions.yml:md5,d2a9a640a711b2d559e13f9bca9d7a3b" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-11T10:47:43.954466231" + "timestamp": "2024-11-04T16:18:47.369135866" }, "severus, fasta, svdb, vep_cache, '110', vep_plugins": { "content": [ [ "versions.yml:md5,84c59e3a0a183b01a21620b16ee9ca4d", "versions.yml:md5,8b626b9e41c9e6de6edc8f94e0e75aed", - "versions.yml:md5,cb83982d3231b281882f4ddc478d93ae" + "versions.yml:md5,d2a9a640a711b2d559e13f9bca9d7a3b" ], "28e9be031273d5e4a94a8654da6e56ed", "test_svs_cnvs_merged_annotated.vcf.gz.tbi" @@ -27,6 +27,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-28T18:04:07.763426107" + "timestamp": "2024-11-04T16:18:35.246526033" } } \ No newline at end of file diff --git a/subworkflows/local/call_cnvs/tests/main.nf.test b/subworkflows/local/call_cnvs/tests/main.nf.test index ad618567..3341f7c2 100644 --- a/subworkflows/local/call_cnvs/tests/main.nf.test +++ b/subworkflows/local/call_cnvs/tests/main.nf.test @@ -43,8 +43,8 @@ nextflow_workflow { """ } } - run("DEEPVARIANT") { - script "../../../../modules/nf-core/deepvariant/main.nf" + run("DEEPVARIANT_RUNDEEPVARIANT") { + script "../../../../modules/nf-core/deepvariant/rundeepvariant/main.nf" process { """ input[0] = MINIMAP2_ALIGN.out.bam @@ -99,7 +99,7 @@ nextflow_workflow { """ input[0] = MINIMAP2_ALIGN.out.bam .join(MINIMAP2_ALIGN.out.index) - .join(DEEPVARIANT.out.vcf) + .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf) input[1] = GUNZIP.out.gunzip input[2] = [[],[]] input[3] = [[],[]] @@ -131,7 +131,7 @@ nextflow_workflow { """ input[0] = MINIMAP2_ALIGN.out.bam .join(MINIMAP2_ALIGN.out.index) - .join(DEEPVARIANT.out.vcf) + .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf) input[1] = GUNZIP.out.gunzip input[2] = [ [ id: 'xy_bed' ], @@ -200,7 +200,7 @@ nextflow_workflow { """ input[0] = MINIMAP2_ALIGN.out.bam .join(MINIMAP2_ALIGN.out.index) - .join(DEEPVARIANT.out.vcf) + .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf) input[1] = GUNZIP.out.gunzip input[2] = [[],[]] input[3] = [[],[]] @@ -226,7 +226,7 @@ nextflow_workflow { """ input[0] = MINIMAP2_ALIGN.out.bam .join(MINIMAP2_ALIGN.out.index) - .join(DEEPVARIANT.out.vcf) + .join(DEEPVARIANT_RUNDEEPVARIANT.out.vcf) input[1] = GUNZIP.out.gunzip input[2] = [ [ id: 'xy_bed' ], diff --git a/subworkflows/local/call_cnvs/tests/nextflow.config b/subworkflows/local/call_cnvs/tests/nextflow.config index 8b89208c..d5ce57da 100644 --- a/subworkflows/local/call_cnvs/tests/nextflow.config +++ b/subworkflows/local/call_cnvs/tests/nextflow.config @@ -2,7 +2,7 @@ process { withName: 'MINIMAP2_ALIGN' { ext.args = '-x map-hifi' } - withName: 'DEEPVARIANT' { + withName: 'DEEPVARIANT_RUNDEEPVARIANT' { ext.args = '--model_type PACBIO' } withName: 'CALL_CNVS:HIFICNV' { diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 768fb131..196b8825 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -6,17 +6,17 @@ "65999ab8f2bc7841de8172468bf23ab6", [ "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", - "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", + "versions.yml:md5,78d86f9ddc871705ca029444a498322f", "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", - "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", - "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" + "versions.yml:md5,b9424dde80b33e84164cc956a14aa459", + "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T10:47:08.425030144" + "timestamp": "2024-11-04T16:23:30.11542862" }, "[bam, bai], fasta, fai, bed - stub": { "content": [ @@ -64,10 +64,10 @@ ], "4": [ "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", - "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", + "versions.yml:md5,78d86f9ddc871705ca029444a498322f", "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", - "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", - "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" + "versions.yml:md5,b9424dde80b33e84164cc956a14aa459", + "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206" ], "project_vcf": [ [ @@ -112,10 +112,10 @@ ], "versions": [ "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", - "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", + "versions.yml:md5,78d86f9ddc871705ca029444a498322f", "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", - "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", - "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" + "versions.yml:md5,b9424dde80b33e84164cc956a14aa459", + "versions.yml:md5,d7098c270381ae9c3c54fd4224f50206" ] } ], @@ -123,6 +123,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-30T11:00:04.845039812" + "timestamp": "2024-11-04T16:23:42.483750233" } -} \ No newline at end of file +} diff --git a/subworkflows/local/methylation/tests/nextflow.config b/subworkflows/local/methylation/tests/nextflow.config index 45b920fe..b977ef2a 100644 --- a/subworkflows/local/methylation/tests/nextflow.config +++ b/subworkflows/local/methylation/tests/nextflow.config @@ -5,7 +5,7 @@ params { process { - withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT' { + withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' { ext.args = { [ '--model_type PACBIO', "--sample_name=${meta.id}", diff --git a/subworkflows/local/rank_variants/tests/nextflow.config b/subworkflows/local/rank_variants/tests/nextflow.config index 3c7e24d0..60f0bcf9 100644 --- a/subworkflows/local/rank_variants/tests/nextflow.config +++ b/subworkflows/local/rank_variants/tests/nextflow.config @@ -4,7 +4,7 @@ process { ext.prefix = { "${name}".contains('merged') ? './vep_cache/homo_sapiens_merged/' : './vep_cache/homo_sapiens/' } } - withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT' { + withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' { ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } ext.args = { [ '--model_type WGS', diff --git a/subworkflows/local/short_variant_calling/main.nf b/subworkflows/local/short_variant_calling/main.nf index c155ac14..d7183dca 100644 --- a/subworkflows/local/short_variant_calling/main.nf +++ b/subworkflows/local/short_variant_calling/main.nf @@ -6,7 +6,7 @@ include { BCFTOOLS_CONCAT } from '../../../modules/n include { BCFTOOLS_FILLTAGS } from '../../../modules/local/bcftools/filltags/main' include { BCFTOOLS_NORM as BCFTOOLS_NORM_MULTISAMPLE } from '../../../modules/nf-core/bcftools/norm/main' include { BCFTOOLS_NORM as BCFTOOLS_NORM_SINGLESAMPLE } from '../../../modules/nf-core/bcftools/norm/main' -include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant/main' +include { DEEPVARIANT_RUNDEEPVARIANT } from '../../../modules/nf-core/deepvariant/rundeepvariant/main' include { DEEPVARIANT_VCFSTATSREPORT } from '../../../modules/nf-core/deepvariant/vcfstatsreport/main' include { GLNEXUS } from '../../../modules/nf-core/glnexus/main' @@ -29,18 +29,18 @@ workflow SHORT_VARIANT_CALLING { } .set { ch_deepvariant_in } - DEEPVARIANT ( ch_deepvariant_in, ch_fasta, ch_fai, [[],[]], ch_par_bed ) - ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) + DEEPVARIANT_RUNDEEPVARIANT ( ch_deepvariant_in, ch_fasta, ch_fai, [[],[]], ch_par_bed ) + ch_versions = ch_versions.mix(DEEPVARIANT_RUNDEEPVARIANT.out.versions) // First remove region so we can group per sample // Then after grouping remove num_intervals since to match the meta of other workflows - DEEPVARIANT.out.vcf + DEEPVARIANT_RUNDEEPVARIANT.out.vcf .map { meta, vcf -> new_meta = meta - meta.subMap('region') [ groupKey(new_meta, new_meta.num_intervals ), vcf ] } .groupTuple() - .join( DEEPVARIANT.out.vcf_tbi + .join( DEEPVARIANT_RUNDEEPVARIANT.out.vcf_tbi .map{ meta, tbi -> new_meta = meta - meta.subMap('region') [ groupKey(new_meta, new_meta.num_intervals ), tbi ] @@ -62,7 +62,7 @@ workflow SHORT_VARIANT_CALLING { ch_versions = ch_versions.mix(BCFTOOLS_NORM_SINGLESAMPLE.out.versions) // This creates a multisample VCF, with regions from ONE bed file - DEEPVARIANT.out.gvcf + DEEPVARIANT_RUNDEEPVARIANT.out.gvcf .map { meta, gvcf -> [ meta.region.name, meta.project, meta.phenotype == 2, gvcf ] } diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap index d084a601..9e8570ee 100644 --- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap +++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap @@ -51,12 +51,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -108,12 +108,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -122,7 +122,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:07:40.986337827" + "timestamp": "2024-11-04T16:32:32.7841728" }, "1 sample - 2 bed, fasta, fai, bed, [] - stub": { "content": [ @@ -193,8 +193,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", @@ -203,6 +201,8 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -271,8 +271,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", @@ -281,6 +279,8 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -289,7 +289,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:10:40.730903286" + "timestamp": "2024-11-04T16:36:05.888336005" }, "1 sample - 1 bed, fasta, fai, bed, []": { "content": [ @@ -343,12 +343,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -400,12 +400,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -414,7 +414,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:08:11.306771116" + "timestamp": "2024-11-04T16:33:12.370911679" }, "2 samples - 2 bed, fasta, fai, bed, par_bed": { "content": [ @@ -506,10 +506,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -520,6 +516,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], @@ -610,10 +610,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -624,6 +620,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] @@ -633,7 +633,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:09:53.140402914" + "timestamp": "2024-11-04T16:35:11.690919461" }, "2 samples - 2 bed, fasta, fai, bed, [] - stub": { "content": [ @@ -725,10 +725,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -739,6 +735,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], @@ -829,10 +829,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -843,6 +839,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] @@ -852,7 +852,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:10:54.089846948" + "timestamp": "2024-11-04T16:36:19.778517029" }, "2 samples - 2 bed, fasta, fai, bed, par_bed - stub": { "content": [ @@ -944,10 +944,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -958,6 +954,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], @@ -1048,10 +1048,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -1062,6 +1058,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] @@ -1071,7 +1071,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:11:07.961520037" + "timestamp": "2024-11-04T16:36:33.89917989" }, "1 sample - 1 bed, fasta, fai, bed, [] - stub": { "content": [ @@ -1125,12 +1125,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -1182,12 +1182,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -1196,7 +1196,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:10:27.465086494" + "timestamp": "2024-11-04T16:35:53.449459889" }, "1 sample - no bed, fasta, fai, [], []": { "content": [ @@ -1254,12 +1254,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -1315,12 +1315,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -1329,7 +1329,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:07:10.788542987" + "timestamp": "2024-11-04T16:31:59.210062583" }, "1 sample - 2 bed, fasta, fai, bed, []": { "content": [ @@ -1400,8 +1400,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", @@ -1410,6 +1408,8 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -1478,8 +1478,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", @@ -1488,6 +1486,8 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -1496,7 +1496,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:08:43.412821579" + "timestamp": "2024-11-04T16:33:50.391467443" }, "2 samples - 2 bed, fasta, fai, bed, []": { "content": [ @@ -1588,10 +1588,6 @@ "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -1602,6 +1598,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], @@ -1692,10 +1692,6 @@ "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", @@ -1706,6 +1702,10 @@ "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] @@ -1715,7 +1715,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:09:18.071239185" + "timestamp": "2024-11-04T16:34:29.736634447" }, "1 sample - no bed, fasta, fai, [], [] - stub": { "content": [ @@ -1773,12 +1773,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -1834,12 +1834,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -1848,7 +1848,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:10:04.450948339" + "timestamp": "2024-11-04T16:35:27.990658402" }, "1 sample - 1 bed, fasta, fai, [], [] - stub": { "content": [ @@ -1902,12 +1902,12 @@ ], "5": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ], "combined_bcf": [ @@ -1959,12 +1959,12 @@ ], "versions": [ "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34", - "versions.yml:md5,13101c9283d4a82e859574b0a981311c", "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44", "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022", "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d", "versions.yml:md5,b461c4ef2d44da4047b74239461bdff6", "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6", + "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0", "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531" ] } @@ -1973,6 +1973,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-29T16:10:15.936988344" + "timestamp": "2024-11-04T16:35:41.50464501" } } \ No newline at end of file diff --git a/subworkflows/local/short_variant_calling/tests/nextflow.config b/subworkflows/local/short_variant_calling/tests/nextflow.config index 613c9e07..2b85525c 100644 --- a/subworkflows/local/short_variant_calling/tests/nextflow.config +++ b/subworkflows/local/short_variant_calling/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT' { + withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' { ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } ext.args = { [ '--model_type WGS', diff --git a/subworkflows/local/snv_annotation/tests/nextflow.config b/subworkflows/local/snv_annotation/tests/nextflow.config index 746f9c59..62fc7b69 100644 --- a/subworkflows/local/snv_annotation/tests/nextflow.config +++ b/subworkflows/local/snv_annotation/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: 'DEEPVARIANT' { + withName: 'DEEPVARIANT_RUNDEEPVARIANT' { ext.prefix = { intervals ? "${meta.id}_${intervals}_deepvariant" : "${meta.id}_deepvariant" } ext.args = { [ '--model_type WGS', diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a..0fcbf7b3 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca..5cb7bafe 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/tests/.nftignore b/tests/.nftignore index 0999bb4a..827e5c29 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -4,7 +4,13 @@ multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_somalier.txt +multiqc/multiqc_data/somalier_*_plot.txt multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt +multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt +multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt +multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt +multiqc/multiqc_plots/**/*.{pdf,svg,txt,png} multiqc/multiqc_report.html paraphase/**/*.{vcf.gz,tbi,bam,bai,json} phased_variants/**/*.{vcf.gz,tbi} diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap index 9e77b8bc..c2e1374c 100644 --- a/tests/samplesheet.nf.test.snap +++ b/tests/samplesheet.nf.test.snap @@ -69,7 +69,7 @@ "CREATE_SAMPLES_FILE": { "gawk": "5.1.0" }, - "DEEPVARIANT": { + "DEEPVARIANT_RUNDEEPVARIANT": { "deepvariant": "1.6.1" }, "DEEPVARIANT_VCFSTATSREPORT": { @@ -155,25 +155,25 @@ "python": "3.8.3" }, "SAMTOOLS_FAIDX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IMPORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_DIPCALL": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_LONGPHASE": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_TRGT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT_TRGT": { - "samtools": 1.2 + "samtools": 1.21 }, "SEVERUS": { "severus": 1.1 @@ -196,7 +196,7 @@ "split_bed_chunks": 1.0 }, "STRANGER": { - "stranger": "0.9.1" + "stranger": "0.9.2" }, "SVDB_MERGE": { "svdb": "2.8.2", @@ -281,6 +281,25 @@ "methylation/modkit/pileup/HG002_Revio/HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi", "multiqc", "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/mosdepth-coverage-per-contig-multi.txt", + "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt", "multiqc/multiqc_data/mosdepth_cov_dist.txt", "multiqc/multiqc_data/mosdepth_cumcov_dist.txt", "multiqc/multiqc_data/mosdepth_perchrom.txt", @@ -293,8 +312,97 @@ "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_somalier.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/multiqc_whatshap_phased_bp_plot.txt", "multiqc/multiqc_data/multiqc_whatshap_stats.txt", + "multiqc/multiqc_data/somalier_het_check_plot.txt", + "multiqc/multiqc_data/somalier_sex_check_plot.txt", + "multiqc/multiqc_data/somalier_stats.txt", + "multiqc/multiqc_data/whatshap-stats-table.txt", "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-cnt.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-log.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", + "multiqc/multiqc_plots/pdf/multiqc_whatshap_phased_bp_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_het_check_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_sex_check_plot.pdf", + "multiqc/multiqc_plots/pdf/whatshap-stats-table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-cnt.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-log.png", + "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", + "multiqc/multiqc_plots/png/multiqc_whatshap_phased_bp_plot.png", + "multiqc/multiqc_plots/png/somalier_het_check_plot.png", + "multiqc/multiqc_plots/png/somalier_sex_check_plot.png", + "multiqc/multiqc_plots/png/whatshap-stats-table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-cnt.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-log.svg", + "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/multiqc_whatshap_phased_bp_plot.svg", + "multiqc/multiqc_plots/svg/somalier_het_check_plot.svg", + "multiqc/multiqc_plots/svg/somalier_sex_check_plot.svg", + "multiqc/multiqc_plots/svg/whatshap-stats-table.svg", "multiqc/multiqc_report.html", "paraphase", "paraphase/HG002_Revio", @@ -422,14 +530,32 @@ "HG002_Revio_modkit_pileup_2.bed.gz.tbi:md5,2ad55c2f604cbdf6a784b2dd99b25cb1", "HG002_Revio_modkit_pileup_ungrouped.bed.gz:md5,04ee840c02e04238b9432bc374a1afe1", "HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi:md5,e1418c8075da8831a52e0cd56ceb910e", - "mosdepth_cov_dist.txt:md5,62011d1135dafcf05d7f6d5750d20c9f", + "bcftools-stats-subtypes.txt:md5,2c23b13117d584b4f424c2bc56dfa4ba", + "bcftools_stats_indel-lengths.txt:md5,bea599c38615af6a033ea3a4436d52c5", + "fastqc-status-check-heatmap.txt:md5,f98c3e5395cfd3061b3228a97ba86043", + "fastqc_adapter_content_plot.txt:md5,85e76640241ce1fd8e3bbf42eb3fa447", + "fastqc_per_base_n_content_plot.txt:md5,c9e46e2888289c319e1b9f412cb0d8e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,6900fc0ad6d05cc49412c9a169473ea8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,4f7571e0b1ef7c917054325aff07d96f", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,70bb2678985be387db93805d5e9fbf2f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,f45a447b91a80e8c6d69607057c828fa", + "fastqc_sequence_counts_plot.txt:md5,464423ea1a9c9db427b47df6f441c079", + "fastqc_sequence_duplication_levels_plot.txt:md5,3da083f3e5e3c37d8ba3d766c5ef2b85", + "fastqc_sequence_length_distribution_plot.txt:md5,014a4c2dbe604408e7b0c359252016f1", + "fastqc_top_overrepresented_sequences_table.txt:md5,21d4be95f2fc981c3f5f8fbe1855bf53", + "mosdepth-coverage-per-contig-multi.txt:md5,39f24c236ea9413f3835ddf24eea86a8", + "mosdepth-cumcoverage-dist-id.txt:md5,ae88f53eaadf28d333f1fbd490d38725", + "mosdepth_cov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413", "mosdepth_cumcov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413", "mosdepth_perchrom.txt:md5,53806d793d5627e60648daebb6606723", "multiqc_bcftools_stats.txt:md5,09a616618fb506994ce178d32325159f", "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350", - "multiqc_fastqc.txt:md5,f0717ca13d848aa8f5eaa5d0dba92178", - "multiqc_general_stats.txt:md5,c82b773e9d5ab3251280f3f03f35193a", + "multiqc_fastqc.txt:md5,8c0330b85e73f68610d35dd71f234cce", + "multiqc_general_stats.txt:md5,8ead46d7d8d14fc8892789a40193646f", + "multiqc_whatshap_phased_bp_plot.txt:md5,41dcd2951f7a6f925f64519491c18d45", "multiqc_whatshap_stats.txt:md5,c8c212ecc6fbf6803f8de87f2395363f", + "somalier_stats.txt:md5,150fa6b9c197c539947168c11d2115f9", + "whatshap-stats-table.txt:md5,c89df1fe6abe77dcbfce8e443c1cecde", "FAM.ped:md5,bd5cec27ba7337a85cf98e787131e2b5", "test.ped:md5,bd5cec27ba7337a85cf98e787131e2b5", "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a", @@ -544,6 +670,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-05T13:41:06.05402932" + "timestamp": "2024-11-06T10:59:47.782981349" } } \ No newline at end of file diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap index 8c4a97ed..bd8ef294 100644 --- a/tests/samplesheet_multisample_bam.nf.test.snap +++ b/tests/samplesheet_multisample_bam.nf.test.snap @@ -69,7 +69,7 @@ "CREATE_SAMPLES_FILE": { "gawk": "5.1.0" }, - "DEEPVARIANT": { + "DEEPVARIANT_RUNDEEPVARIANT": { "deepvariant": "1.6.1" }, "DEEPVARIANT_VCFSTATSREPORT": { @@ -155,22 +155,22 @@ "python": "3.8.3" }, "SAMTOOLS_FAIDX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_FASTQ": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_DIPCALL": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_TRGT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT_TRGT": { - "samtools": 1.2 + "samtools": 1.21 }, "SEVERUS": { "severus": 1.1 @@ -193,7 +193,7 @@ "split_bed_chunks": 1.0 }, "STRANGER": { - "stranger": "0.9.1" + "stranger": "0.9.2" }, "SVDB_MERGE": { "svdb": "2.8.2", @@ -306,6 +306,26 @@ "methylation/modkit/pileup/HG002_Revio_B/HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi", "multiqc", "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/mosdepth-coverage-per-contig-multi.txt", + "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt", "multiqc/multiqc_data/mosdepth_cov_dist.txt", "multiqc/multiqc_data/mosdepth_cumcov_dist.txt", "multiqc/multiqc_data/mosdepth_perchrom.txt", @@ -318,8 +338,108 @@ "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_somalier.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/multiqc_whatshap_phased_bp_plot.txt", "multiqc/multiqc_data/multiqc_whatshap_stats.txt", + "multiqc/multiqc_data/somalier_het_check_plot.txt", + "multiqc/multiqc_data/somalier_relatedness_heatmap_plot.txt", + "multiqc/multiqc_data/somalier_relatedness_plot.txt", + "multiqc/multiqc_data/somalier_sex_check_plot.txt", + "multiqc/multiqc_data/somalier_stats.txt", + "multiqc/multiqc_data/whatshap-stats-table.txt", "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-cnt.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-log.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", + "multiqc/multiqc_plots/pdf/multiqc_whatshap_phased_bp_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_het_check_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_relatedness_heatmap_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_relatedness_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_sex_check_plot.pdf", + "multiqc/multiqc_plots/pdf/whatshap-stats-table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-cnt.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-log.png", + "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", + "multiqc/multiqc_plots/png/multiqc_whatshap_phased_bp_plot.png", + "multiqc/multiqc_plots/png/somalier_het_check_plot.png", + "multiqc/multiqc_plots/png/somalier_relatedness_heatmap_plot.png", + "multiqc/multiqc_plots/png/somalier_relatedness_plot.png", + "multiqc/multiqc_plots/png/somalier_sex_check_plot.png", + "multiqc/multiqc_plots/png/whatshap-stats-table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-cnt.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-log.svg", + "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/multiqc_whatshap_phased_bp_plot.svg", + "multiqc/multiqc_plots/svg/somalier_het_check_plot.svg", + "multiqc/multiqc_plots/svg/somalier_relatedness_heatmap_plot.svg", + "multiqc/multiqc_plots/svg/somalier_relatedness_plot.svg", + "multiqc/multiqc_plots/svg/somalier_sex_check_plot.svg", + "multiqc/multiqc_plots/svg/whatshap-stats-table.svg", "multiqc/multiqc_report.html", "paraphase", "paraphase/HG002_Revio_A", @@ -529,14 +649,33 @@ "HG002_Revio_B_modkit_pileup_2.bed.gz.tbi:md5,d1c192d65d8fa8cbb8ffa2e545282fde", "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz:md5,49d9380eb739081b7a0b4dfa7756d09c", "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,f569a923cc5204df5dc495354ab83a13", - "mosdepth_cov_dist.txt:md5,41793745406425cfa02d558875df8d16", + "bcftools-stats-subtypes.txt:md5,5b9c985c35950dfb8cd7827fc8d524c4", + "bcftools_stats_indel-lengths.txt:md5,9272a5340f808c3f5874f1b2fd18da6c", + "fastqc-status-check-heatmap.txt:md5,20c6520b895e05df6cfeab492819e94a", + "fastqc_adapter_content_plot.txt:md5,8f9e7b3e1e31caeb58b0fbf31624ea53", + "fastqc_overrepresented_sequences_plot.txt:md5,9b021bffa0a2d100fdbe637fa7c40a62", + "fastqc_per_base_n_content_plot.txt:md5,47f64b0eb087268bae1d1172c4ce31d6", + "fastqc_per_base_sequence_quality_plot.txt:md5,a3d1e7e58b6c859a06f661f01f920ce7", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,cfbe632f2c5e4a519381c3e3e807909f", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,1172a95a897c2f171dab3d12ce10a70a", + "fastqc_per_sequence_quality_scores_plot.txt:md5,89d24f2fe5c673e9dcf3dbb97e4aa477", + "fastqc_sequence_counts_plot.txt:md5,70873e76a534c7a52c0fc5a87a071121", + "fastqc_sequence_duplication_levels_plot.txt:md5,af3f96831de8d9953021be605fea74cd", + "fastqc_sequence_length_distribution_plot.txt:md5,f857786dd1f7dba0aa558980009d19d4", + "fastqc_top_overrepresented_sequences_table.txt:md5,966e1c4f34623fbf427d2ce5d1adf926", + "mosdepth-coverage-per-contig-multi.txt:md5,9ad34655cae2598a7448da87e147643e", + "mosdepth-cumcoverage-dist-id.txt:md5,f82fef24eefb391616c07268fcc826b4", + "mosdepth_cov_dist.txt:md5,c53933e0b572d115ecd35a5adb3e0a04", "mosdepth_cumcov_dist.txt:md5,c53933e0b572d115ecd35a5adb3e0a04", "mosdepth_perchrom.txt:md5,9fd9c40c7a6be06a338f2039a5d91fb8", "multiqc_bcftools_stats.txt:md5,dbbc176792fbf2845547dfdcd39fc208", "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350", - "multiqc_fastqc.txt:md5,18ca1a3fb2afa8988dc5d604c049cd9c", - "multiqc_general_stats.txt:md5,4a2c114e57d5581b606012d1604d51fa", + "multiqc_fastqc.txt:md5,e466de366de86998b84ba6c25aafafd6", + "multiqc_general_stats.txt:md5,d1bfae61713bed6068386db5cb92cde9", + "multiqc_whatshap_phased_bp_plot.txt:md5,d70d629693c3229c37750440636c0a90", "multiqc_whatshap_stats.txt:md5,96447de4e14a9b4a570c24513de64970", + "somalier_stats.txt:md5,5f523bdaa8f6b6bf1581694564521891", + "whatshap-stats-table.txt:md5,862f90185133703811c955c45f5750fa", "FAM.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4", "test.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4", "HG002_Revio_A_phased.blocks.tsv:md5,27ce044ba581da15ef838cbb343a64cf", @@ -741,6 +880,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-05T13:42:51.526893089" + "timestamp": "2024-11-06T11:01:42.969612471" } } \ No newline at end of file diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap index cf41a33c..abd0e8dd 100644 --- a/tests/samplesheet_multisample_ont_bam.nf.test.snap +++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap @@ -60,7 +60,7 @@ "CREATE_SAMPLES_FILE": { "gawk": "5.1.0" }, - "DEEPVARIANT": { + "DEEPVARIANT_RUNDEEPVARIANT": { "deepvariant": "1.6.1" }, "DEEPVARIANT_VCFSTATSREPORT": { @@ -125,13 +125,13 @@ "python": "3.8.3" }, "SAMTOOLS_FAIDX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX_WHATSHAP": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": 1.2 + "samtools": 1.21 }, "SEVERUS": { "severus": 1.1 @@ -220,6 +220,26 @@ "methylation/modkit/pileup/HG002_ONT_B/HG002_ONT_B_modkit_pileup_ungrouped.bed.gz.tbi", "multiqc", "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/mosdepth-coverage-per-contig-multi.txt", + "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt", "multiqc/multiqc_data/mosdepth_cov_dist.txt", "multiqc/multiqc_data/mosdepth_cumcov_dist.txt", "multiqc/multiqc_data/mosdepth_perchrom.txt", @@ -232,8 +252,108 @@ "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_somalier.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/multiqc_whatshap_phased_bp_plot.txt", "multiqc/multiqc_data/multiqc_whatshap_stats.txt", + "multiqc/multiqc_data/somalier_het_check_plot.txt", + "multiqc/multiqc_data/somalier_relatedness_heatmap_plot.txt", + "multiqc/multiqc_data/somalier_relatedness_plot.txt", + "multiqc/multiqc_data/somalier_sex_check_plot.txt", + "multiqc/multiqc_data/somalier_stats.txt", + "multiqc/multiqc_data/whatshap-stats-table.txt", "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-cnt.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-multi-log.pdf", + "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", + "multiqc/multiqc_plots/pdf/multiqc_whatshap_phased_bp_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_het_check_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_relatedness_heatmap_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_relatedness_plot.pdf", + "multiqc/multiqc_plots/pdf/somalier_sex_check_plot.pdf", + "multiqc/multiqc_plots/pdf/whatshap-stats-table.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", + "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-cnt.png", + "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-multi-log.png", + "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", + "multiqc/multiqc_plots/png/multiqc_whatshap_phased_bp_plot.png", + "multiqc/multiqc_plots/png/somalier_het_check_plot.png", + "multiqc/multiqc_plots/png/somalier_relatedness_heatmap_plot.png", + "multiqc/multiqc_plots/png/somalier_relatedness_plot.png", + "multiqc/multiqc_plots/png/somalier_sex_check_plot.png", + "multiqc/multiqc_plots/png/whatshap-stats-table.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-cnt.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-multi-log.svg", + "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/multiqc_whatshap_phased_bp_plot.svg", + "multiqc/multiqc_plots/svg/somalier_het_check_plot.svg", + "multiqc/multiqc_plots/svg/somalier_relatedness_heatmap_plot.svg", + "multiqc/multiqc_plots/svg/somalier_relatedness_plot.svg", + "multiqc/multiqc_plots/svg/somalier_sex_check_plot.svg", + "multiqc/multiqc_plots/svg/whatshap-stats-table.svg", "multiqc/multiqc_report.html", "paraphase", "paraphase/HG002_ONT_A", @@ -374,14 +494,33 @@ "HG002_ONT_B_modkit_pileup_2.bed.gz.tbi:md5,e6eb3c61b79a4abd0fd952f710d6eab3", "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz:md5,42dcaedf8c379a4e5dee0822d5e8aca4", "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,3d97d016882c99e4e21112fc76ceb2a2", - "mosdepth_cov_dist.txt:md5,1eb2a5c39fd4b8dd814049b65b007037", + "bcftools-stats-subtypes.txt:md5,1a8c8da19e5bc947cfb77de3683c8c00", + "bcftools_stats_indel-lengths.txt:md5,cc976b96114f0b68daffec58a7643d53", + "fastqc-status-check-heatmap.txt:md5,03e5dc3abd2f2599a7bb03739dd5ca86", + "fastqc_adapter_content_plot.txt:md5,00c7bec7dd9304848f7d891d7d1fab7f", + "fastqc_overrepresented_sequences_plot.txt:md5,6f0148406e9d5358bf37375b33a4bc01", + "fastqc_per_base_n_content_plot.txt:md5,8551be865db8162f7d6203e0e34288e0", + "fastqc_per_base_sequence_quality_plot.txt:md5,f5e2e866bebda66cd877522342a2bf8a", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,8f108751cb49e0d80729247b84ddee76", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,2c68289482d7bffc37efe8110eff9328", + "fastqc_per_sequence_quality_scores_plot.txt:md5,eb18c5356c9bf4eae99f0103b04a8a81", + "fastqc_sequence_counts_plot.txt:md5,d80ddc5d3e3810f5bad4e04b85bd3056", + "fastqc_sequence_duplication_levels_plot.txt:md5,005e3c05e83b9e681f7d02709007df15", + "fastqc_sequence_length_distribution_plot.txt:md5,befaab9e643f27b4fc184577e2dd9dda", + "fastqc_top_overrepresented_sequences_table.txt:md5,48a5253938a61c69babe90a5c7c4b862", + "mosdepth-coverage-per-contig-multi.txt:md5,4339c1147fa7ec9059126bf4c8b6760e", + "mosdepth-cumcoverage-dist-id.txt:md5,d18aa3d23b90333c6d6d84bd0510c5c6", + "mosdepth_cov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9", "mosdepth_cumcov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9", "mosdepth_perchrom.txt:md5,86a907217d64d4c2717885403058580f", "multiqc_bcftools_stats.txt:md5,41a78d00bdca33cf0d2a558bb60838db", "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350", - "multiqc_fastqc.txt:md5,5254c5d578af3a24182ccf3248183ac6", - "multiqc_general_stats.txt:md5,0722f1462d3502d5383eb86a484192c6", + "multiqc_fastqc.txt:md5,ce26d17e62f3c8a1c9a01a871a4b9586", + "multiqc_general_stats.txt:md5,0814fb98fbb85e001e9c0c04d586d602", + "multiqc_whatshap_phased_bp_plot.txt:md5,e97b7038c7155326b5d6a2289cc0aeb7", "multiqc_whatshap_stats.txt:md5,5c4b972c8d52b3d997f117b39ba3ad5d", + "somalier_stats.txt:md5,fec840d4fe202c0e3ff7ce94b2a3bf92", + "whatshap-stats-table.txt:md5,d552daaaef1c92c3351ec2f4de64e6ad", "FAM.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12", "test.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12", "HG002_ONT_A_cramino_aligned_phased.arrow:md5,d2a5c81595fa34925ab8f03078487d81", @@ -485,6 +624,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-05T13:44:39.150334649" + "timestamp": "2024-11-06T09:55:21.893675661" } } \ No newline at end of file diff --git a/workflows/nallo.nf b/workflows/nallo.nf index 84aee66d..36b4e37e 100644 --- a/workflows/nallo.nf +++ b/workflows/nallo.nf @@ -177,12 +177,12 @@ workflow NALLO { .set { bam_to_merge } // Merge files if we have multiple files per sample - SAMTOOLS_MERGE ( bam_to_merge.multiple.map { meta, bam, bai -> [ meta, bam ] }, [[],[]], [[],[]], 'bai' ) + SAMTOOLS_MERGE ( bam_to_merge.multiple.map { meta, bam, bai -> [ meta, bam ] }, [[],[]], [[],[]]) ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) // Combine merged with unmerged bams SAMTOOLS_MERGE.out.bam - .join(SAMTOOLS_MERGE.out.index) + .join(SAMTOOLS_MERGE.out.bai) .concat(bam_to_merge.single) .map { meta, bam, bai -> [ meta - meta.subMap('n_files'), bam, bai ] } .set { bam_infer_sex_in } @@ -610,7 +610,9 @@ workflow NALLO { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) emit: