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genomic-medicine-sweden · Nov 5, 2024 · f90fd75 · f90fd75
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Showing 4 changed files with 21 additions and 30 deletions.
diff --git a/docs/output.md b/docs/output.md
@@ -163,21 +163,21 @@ If the pipeline is run with phasing, the aligned reads will be happlotagged usin
 
     Merged variants per family are only output without annotation if `--skip_repeat_annotation` is true. Variants per sample are always output without annotation.
 
-| Path                                                    | Description                               |
-| ------------------------------------------------------- | ----------------------------------------- |
-| `repeats/{family}/{family}_repeat_expansions.vcf.gz`    | Merged VCF file per family                |
-| `repeats/{family}/{family_repeat_expansions.vcf.gz.tbi` | Index of the VCF file                     |
-| `repeats/sample/{sample}/*.vcf.gz`                      | VCF file with called repeats for a sample |
-| `repeats/sample/{sample}/*.vcf.gz.tbi`                  | Index of the VCF file                     |
-| `repeats/sample/{sample}/*.bam`                         | BAM file with sorted spanning reads       |
-| `repeats/sample/{sample}/*.bai`                         | Index of the BAM file                     |
+| Path                                                     | Description                               |
+| -------------------------------------------------------- | ----------------------------------------- |
+| `repeats/{family}/{family}_repeat_expansions.vcf.gz`     | Merged VCF file per family                |
+| `repeats/{family}/{family}_repeat_expansions.vcf.gz.tbi` | Index of the VCF file                     |
+| `repeats/sample/{sample}/{sample}_sorted.vcf.gz`         | VCF file with called repeats for a sample |
+| `repeats/sample/{sample}/{sample}_sorted.vcf.gz.tbi`     | Index of the VCF file                     |
+| `repeats/sample/{sample}/{sample}_spanning_sorted.bam`   | BAM file with sorted spanning reads       |
+| `repeats/sample/{sample}/{sample}_spanning_sorted.bai`   | Index of the BAM file                     |
 
 [Stranger](https://github.com/Clinical-Genomics/stranger) is used to annotate repeats.
 
-| Path                                                                        | Description                           |
-| --------------------------------------------------------------------------- | ------------------------------------- |
-| `repeat_expansions/{family}/{family}_repeat_expansions_annotated.vcf.gz`    | Merged, annotated VCF file per family |
-| `repeat_expansions/{family}/{family_repeat_expansions_annotated.vcf.gz.tbi` | Index of the VCF file                 |
+| Path                                                                         | Description                           |
+| ---------------------------------------------------------------------------- | ------------------------------------- |
+| `repeat_expansions/{family}/{family}_repeat_expansions_annotated.vcf.gz`     | Merged, annotated VCF file per family |
+| `repeat_expansions/{family}/{family}_repeat_expansions_annotated.vcf.gz.tbi` | Index of the VCF file                 |
 
 ### SNVs
 

diff --git a/tests/.nftignore b/tests/.nftignore
@@ -13,7 +13,6 @@ qc/cramino/**/*.txt
 qc/fastqc/**/*.{zip,html}
 qc/somalier/**/*.{html,tsv}
 qc/deepvariant_vcfstatsreport/**/*.html
-repeat_annotation/**/*.{vcf.gz,tbi}
-repeat_calling/**/*.{vcf.gz,tbi,bam,bai}
+repeats/**/*.{vcf.gz,tbi,bam,bai}
 snvs/**/*.{vcf.gz,tbi,txt}
 svs/**/*.{vcf.gz,tbi}
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
@@ -435,12 +435,6 @@
                 "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
                 "HG002_Revio_stats.blocks.tsv:md5,e73960d863a78848498499480ea9937f",
                 "HG002_Revio_stats.stats.tsv:md5,cffa4a500350b2227ab40bbbe428e9ef",
-                "FAM_repeats_annotated.vcf.gz:md5,eefc76d462d032dca899530c9b5d28e3",
-                "FAM_repeats_annotated.vcf.gz.tbi:md5,fc30f983abc683359d12dbfb3e45497d",
-                "HG002_Revio_sorted.vcf.gz:md5,a44d6d7fa3ff96fe1c77f0b045cfb46f",
-                "HG002_Revio_sorted.vcf.gz.tbi:md5,60d7a65d9a296bde30aefa38918feb88",
-                "HG002_Revio_spanning_sorted.bam:md5,468a86260e36702416d8ee01317eda1c",
-                "HG002_Revio_spanning_sorted.bam.bai:md5,6733ea2585a20aaa93aa40b1437e7440",
                 "HG002_Revio_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
                 "HG002_Revio_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
                 "HG002_Revio_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c"
@@ -536,6 +530,10 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
+<<<<<<< HEAD
         "timestamp": "2024-11-05T13:41:06.05402932"
+=======
+        "timestamp": "2024-11-04T17:27:22.813993718"
+>>>>>>> 7691a30 (docs)
     }
 }
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -554,16 +554,6 @@
                 "HG002_Revio_A_stats.stats.tsv:md5,1504949804b510cc57d20e2c78fb7294",
                 "HG002_Revio_B_stats.blocks.tsv:md5,df646f43e67f37df5a9ec148e431d4c3",
                 "HG002_Revio_B_stats.stats.tsv:md5,40994b57e7c0bafee411bc2ad6ffb79d",
-                "FAM_repeats_annotated.vcf.gz:md5,73f3582df9154e936eb523c0b3ea8edb",
-                "FAM_repeats_annotated.vcf.gz.tbi:md5,ef6bee507dcb164cea090fa5d8903dad",
-                "HG002_Revio_A_sorted.vcf.gz:md5,105ece371d6751f331c56734ee1a6b1f",
-                "HG002_Revio_A_sorted.vcf.gz.tbi:md5,7d8c345b22657d134a02d5a450815f99",
-                "HG002_Revio_A_spanning_sorted.bam:md5,7c823225e5598dcb6eef92d6953cdd6f",
-                "HG002_Revio_A_spanning_sorted.bam.bai:md5,1b407bbf2ee1627219e3b251ae385817",
-                "HG002_Revio_B_sorted.vcf.gz:md5,79317b06924078e48f9e69f2ad596351",
-                "HG002_Revio_B_sorted.vcf.gz.tbi:md5,7d8c345b22657d134a02d5a450815f99",
-                "HG002_Revio_B_spanning_sorted.bam:md5,152e46b8c76b5e3ecd01ec3323a83474",
-                "HG002_Revio_B_spanning_sorted.bam.bai:md5,1899c77316d90521e2d28967f35fabf6",
                 "HG002_Revio_A_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
                 "HG002_Revio_A_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
                 "HG002_Revio_A_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c",
@@ -726,6 +716,10 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
+<<<<<<< HEAD
         "timestamp": "2024-11-05T13:42:51.526893089"
+=======
+        "timestamp": "2024-11-04T17:30:31.18296401"
+>>>>>>> 7691a30 (docs)
     }
 }