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nf-core · Feb 16, 2024 · 3099751 · 3099751
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commit 3099751
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/conf/modules/call_snv.config b/conf/modules/call_snv.config
@@ -21,7 +21,7 @@ process {
 
     withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' {
         ext.args   = { "--exclude-intervals ${params.mito_name}" }
-        ext.prefix = { "${meta.id}_nomito" }
+        ext.prefix = { "${meta.id}_snv" }
         publishDir = [
             path: { "${params.outdir}/call_snv/genome" },
             mode: params.publish_dir_mode,

diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config
@@ -19,6 +19,7 @@ process {
 
     withName: '.*CALL_SV_MT:MT_DELETION' {
         ext.args = '-s --insert-size 16000'
+        ext.prefix = { "${meta.id}_mitochondria_deletions" }
         publishDir = [
             path: { "${params.outdir}/call_sv/mitochondria" },
             mode: params.publish_dir_mode,

diff --git a/docs/output.md b/docs/output.md
@@ -266,8 +266,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 <summary>Output files</summary>
 
 - `call_snv/genome`
-  - `<case_id>_nomito.vcf.gz`: normalized vcf file containing no MT variants.
-  - `<case_id>_nomito.vcf.gz.tbi`: index of the vcf file containing no MT variants.
+  - `<case_id>_snv.vcf.gz`: normalized vcf file containing no MT variants.
+  - `<case_id>_snv.vcf.gz.tbi`: index of the vcf file containing no MT variants.
 
 </details>
 
@@ -279,8 +279,8 @@ The pipeline performs variant calling using [Sentieon DNAscope](https://support.
 <summary>Output files</summary>
 
 - `call_snv/genome`
-  - `<case_id>_nomito.vcf.gz`: normalized vcf file containing no MT variants.
-  - `<case_id>_nomito.vcf.gz.tbi`: index of the vcf file containing no MT variants.
+  - `<case_id>_snv.vcf.gz`: normalized vcf file containing no MT variants.
+  - `<case_id>_snv.vcf.gz.tbi`: index of the vcf file containing no MT variants.
 
 </details>
 
@@ -456,7 +456,7 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen
 [MT deletion script](https://github.com/dnil/mitosign/blob/master/run_mt_del_check.sh) lists the fraction of mitochondrially aligning read pairs (per 1000) that appear discordant, as defined by an insert size of more than 1.2 kb (and less than 15 kb due to the circular nature of the genome) using samtools.
 
 - `call_sv/mitochondria`
-  - `<sample_id>.txt`: file containing deletions.
+  - `<sample_id>_mitochondria_deletions.txt`: file containing deletions.
 
 ##### eKLIPse