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[automated] Update json files and markdown cache
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@nf-core-bot
nf-core-bot committed Nov 7, 2024
1 parent 477723a commit 621d7d5
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308 changes: 304 additions & 4 deletions public/components.json
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"@nictru",
"@LeonHafner"
]
}
},
"pipelines": [
{
"name": "scdownstream",
"version": "dev"
}
]
},
{
"name": "annotsv_annotsv",
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"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
},
{
"name": "rnafusion",
"version": "3.0.2"
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"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "pathogensurveillance",
"version": "dev"
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"name": "scnanoseq",
"version": "1.0.0"
},
{
"name": "spatialxe",
"version": "dev"
},
{
"name": "ssds",
"version": "dev"
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"maintainers": [
"@LeonHafner"
]
}
},
"pipelines": [
{
"name": "scdownstream",
"version": "dev"
}
]
},
{
"name": "dragmap_align",
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"name": "spatialvi",
"version": "dev"
},
{
"name": "spatialxe",
"version": "dev"
},
{
"name": "ssds",
"version": "dev"
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]
}
},
{
"name": "hiphase",
"path": "modules/nf-core/hiphase/meta.yml",
"type": "module",
"meta": {
"name": "hiphase",
"description": "pacbio structural variant calling tool",
"keywords": [
"sort",
"example",
"genomics"
],
"tools": [
{
"hiphase": {
"description": "Small and structural variant phasing tool for PacBio HiFi reads",
"homepage": "https://github.com/PacificBiosciences/HiPhase",
"documentation": "https://github.com/PacificBiosciences/HiPhase",
"tool_dev_url": "https://github.com/PacificBiosciences/HiPhase",
"licence": [
"Pacific Biosciences Software License Agreement"
],
"identifier": "biotools:hiphase"
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"vcf": {
"type": "file",
"description": "VCF File",
"pattern": "*.{vcf}"
}
},
{
"csi": {
"type": "file",
"description": "CSI File associated with VCF",
"pattern": "*.{csi}"
}
}
],
[
{
"meta2": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"bam": {
"type": "file",
"description": "Sorted BAM/CRAM/SAM file",
"pattern": "*.{bam}"
}
},
{
"bai": {
"type": "file",
"description": "Index File BAI associated with BAM file",
"pattern": "*.{bai}"
}
}
],
[
{
"meta3": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"fasta": {
"type": "file",
"description": "FASTA File (used for the alignment of the BAM file)",
"pattern": "*.{fasta}"
}
}
]
],
"output": [
{
"vcf": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.vcf": {
"type": "file",
"description": "Phased VCF file",
"pattern": "*.vcf"
}
}
]
},
{
"csv": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.csv": {
"type": "file",
"description": "stats associated with the phasing",
"pattern": "*.csv"
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@tanyasarkjain"
],
"maintainers": [
"@tanyasarkjain"
]
}
},
{
"name": "hisat2_align",
"path": "modules/nf-core/hisat2/align/meta.yml",
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"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
},
{
"name": "genomeassembler",
"version": "dev"
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]
}
},
{
"name": "metamdbg_asm",
"path": "modules/nf-core/metamdbg/asm/meta.yml",
"type": "module",
"meta": {
"name": "METAMDBG_ASM",
"description": "Metagenome assembler for long-read sequences (HiFi and ONT).",
"keywords": [
"assembly",
"long reads",
"metagenome",
"metagenome assembler"
],
"tools": [
{
"metamdbg": {
"description": "MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.",
"homepage": "https://github.com/GaetanBenoitDev/metaMDBG",
"documentation": "https://github.com/GaetanBenoitDev/metaMDBG",
"tool_dev_url": "https://github.com/GaetanBenoitDev/metaMDBG",
"doi": "10.1038/s41587-023-01983-6",
"licence": [
"MIT"
],
"identifier": ""
}
}
],
"input": [
[
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"reads": {
"type": "file",
"description": "Long read sequence data from ONT or HiFi in fasta format (can be gzipped)",
"pattern": "*.{fa,fasta,fa.gz,fasta.gz}"
}
}
],
[
{
"input_type": {
"type": "string",
"description": "Sequencing technology for reads - either \"hifi\" for PacBio HiFi reads or \"ont\" for Oxford Nanopore reads."
}
}
]
],
"output": [
{
"contigs": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.contigs.fasta.gz": {
"type": "file",
"description": "Gzipped fasta file containing the assembled contigs from the input\nreads.\n"
}
}
]
},
{
"log": [
{
"meta": {
"type": "map",
"description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
}
},
{
"*.metaMDBG.log": {
"type": "file",
"description": "Log file describing the metaMDBG run."
}
}
]
},
{
"versions": [
{
"versions.yml": {
"type": "file",
"description": "File containing software versions",
"pattern": "versions.yml"
}
}
]
}
],
"authors": [
"@prototaxites"
],
"maintainers": [
"@prototaxites"
]
}
},
{
"name": "metaphlan3_mergemetaphlantables",
"path": "modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml",
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"name": "spatialvi",
"version": "dev"
},
{
"name": "spatialxe",
"version": "dev"
},
{
"name": "ssds",
"version": "dev"
Expand Down Expand Up @@ -155800,7 +156088,13 @@
"maintainers": [
"@nictru"
]
}
},
"pipelines": [
{
"name": "scdownstream",
"version": "dev"
}
]
},
{
"name": "scvitools_solo",
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"maintainers": [
"@LeonHafner"
]
}
},
"pipelines": [
{
"name": "scdownstream",
"version": "dev"
}
]
},
{
"name": "seacr_callpeak",
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2 changes: 1 addition & 1 deletion public/pipeline_names.json
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@@ -1 +1 @@
{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","deepmodeloptim","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastqrepair","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeqc","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]}
{"pipeline":["airrflow","ampliseq","atacseq","bacass","bactmap","bamtofastq","cageseq","callingcards","chipseq","circdna","circrna","clipseq","coproid","createpanelrefs","createtaxdb","crisprseq","cutandrun","datasync","deepmodeloptim","demo","demultiplex","denovotranscript","detaxizer","diaproteomics","differentialabundance","drugresponseeval","dualrnaseq","eager","epitopeprediction","fastqrepair","fastquorum","fetchngs","funcscan","genomeannotator","genomeassembler","genomeqc","genomeskim","gwas","hgtseq","hic","hicar","hlatyping","imcyto","isoseq","lncpipe","mag","magmap","marsseq","mcmicro","meerpipe","metaboigniter","metapep","metatdenovo","methylarray","methylseq","mhcquant","mnaseseq","molkart","multiplesequencealign","nanoseq","nanostring","nascent","omicsgenetraitassociation","oncoanalyser","pairgenomealign","pangenome","pathogensurveillance","pgdb","phageannotator","phaseimpute","phyloplace","pixelator","proteinfold","proteomicslfq","radseq","rangeland","raredisease","readsimulator","reportho","riboseq","rnadnavar","rnafusion","rnaseq","rnasplice","rnavar","sammyseq","sarek","scdownstream","scnanoseq","scrnaseq","seqinspector","slamseq","smrnaseq","spatialvi","spatialxe","spinningjenny","taxprofiler","tbanalyzer","tfactivity","troughgraph","variantbenchmarking","variantcatalogue","viralintegration","viralrecon"]}
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