Merge pull request nf-core#657 from nf-core/fix_samplename

Remove suffixes sample name in repeat call vcfs
genomic-medicine-sweden · Jan 8, 2025 · 8ea8d23 · 8ea8d23
2 parents 1e410c6 + b619087
commit 8ea8d23
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Showing 2 changed files with 26 additions and 12 deletions.
diff --git a/modules/local/rename_align_files.nf b/modules/local/rename_align_files.nf
@@ -12,7 +12,7 @@ process RENAME_ALIGN_FILES {
     val(extension)
 
     output:
-    path("*.{bam,bai}"), emit: output
+    tuple val(meta), path("*.{bam,bai}"), emit: output
     path "versions.yml", emit: versions
 
     when:

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -127,10 +127,10 @@ include { SMNCOPYNUMBERCALLER } from '../modules/nf-core/smncopynumbercaller/mai
 // MODULE: Local modules
 //
 
-include { RENAME_ALIGN_FILES as RENAME_BAM_FOR_SMNCALLER } from '../modules/local/rename_align_files'
-include { RENAME_ALIGN_FILES as RENAME_BAI_FOR_SMNCALLER } from '../modules/local/rename_align_files'
-include { CREATE_HGNCIDS_FILE                            } from '../modules/local/create_hgncids_file'
-include { CREATE_PEDIGREE_FILE                           } from '../modules/local/create_pedigree_file'
+include { RENAME_ALIGN_FILES as RENAME_BAM } from '../modules/local/rename_align_files'
+include { RENAME_ALIGN_FILES as RENAME_BAI } from '../modules/local/rename_align_files'
+include { CREATE_HGNCIDS_FILE              } from '../modules/local/create_hgncids_file'
+include { CREATE_PEDIGREE_FILE             } from '../modules/local/create_pedigree_file'
 
 //
 // SUBWORKFLOWS
@@ -464,6 +464,18 @@ workflow RAREDISEASE {
     )
     ch_versions = ch_versions.mix(QC_BAM.out.versions)
 
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RENAME ALIGNMENT FILES FOR SMNCOPYNUMBERCALLER & REPEATCALLING
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+    if ( params.analysis_type.equals("wgs") && (!params.skip_smncopynumbercaller || !params.skip_repeat_calling)) {
+        RENAME_BAM(ch_mapped.genome_marked_bam, "bam")
+        RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai")
+    }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     CALL AND ANNOTATE REPEAT EXPANSIONS
@@ -472,7 +484,7 @@ workflow RAREDISEASE {
 
     if (!params.skip_repeat_calling && params.analysis_type.equals("wgs") ) {
         CALL_REPEAT_EXPANSIONS (
-            ch_mapped.genome_bam_bai,
+            RENAME_BAM.out.output.join(RENAME_BAI.out.output, failOnMismatch:true, failOnDuplicate:true),
             ch_variant_catalog,
             ch_case_info,
             ch_genome_fasta,
@@ -766,13 +778,14 @@ workflow RAREDISEASE {
 */
 
     if ( params.analysis_type.equals("wgs") && !params.skip_smncopynumbercaller ) {
-        RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
-            .collect{it}
+
+        RENAME_BAM.out.output
+            .collect{it[1]}
             .toList()
             .set { ch_bam_list }
 
-        RENAME_BAI_FOR_SMNCALLER(ch_mapped.genome_marked_bai, "bam.bai").output
-            .collect{it}
+        RENAME_BAI.out.output
+            .collect{it[1]}
             .toList()
             .set { ch_bai_list }
 
@@ -784,10 +797,11 @@ workflow RAREDISEASE {
         SMNCOPYNUMBERCALLER (
             ch_bams_bais
         )
-        ch_versions = ch_versions.mix(RENAME_BAM_FOR_SMNCALLER.out.versions)
-        ch_versions = ch_versions.mix(RENAME_BAI_FOR_SMNCALLER.out.versions)
+        ch_versions = ch_versions.mix(RENAME_BAM.out.versions)
+        ch_versions = ch_versions.mix(RENAME_BAI.out.versions)
         ch_versions = ch_versions.mix(SMNCOPYNUMBERCALLER.out.versions)
     }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     PEDDY