update rename module

nf-core · Jan 7, 2025 · 3fbae07 · 3fbae07
1 parent 06b8c2e
commit 3fbae07
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Showing 2 changed files with 19 additions and 16 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
@@ -472,20 +472,8 @@ workflow RAREDISEASE {
 */
 
     if ( params.analysis_type.equals("wgs") && (!params.skip_smncopynumbercaller || !params.skip_repeat_calling)) {
-        RENAME_BAM(ch_mapped.genome_marked_bam, "bam").output
-            .collect{it}
-            .toList()
-            .set { ch_bam_list }
-
-        RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai").output
-            .collect{it}
-            .toList()
-            .set { ch_bai_list }
-
-        ch_case_info
-            .combine(ch_bam_list)
-            .combine(ch_bai_list)
-            .set { ch_bams_bais }
+        RENAME_BAM(ch_mapped.genome_marked_bam, "bam")
+        RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai")
     }
 
 /*
@@ -496,7 +484,7 @@ workflow RAREDISEASE {
 
     if (!params.skip_repeat_calling && params.analysis_type.equals("wgs") ) {
         CALL_REPEAT_EXPANSIONS (
-            ch_bams_bais,
+            RENAME_BAM.out.output.join(RENAME_BAI.out.output, failOnMismatch:true, failOnDuplicate:true),
             ch_variant_catalog,
             ch_case_info,
             ch_genome_fasta,
@@ -791,6 +779,21 @@ workflow RAREDISEASE {
 
     if ( params.analysis_type.equals("wgs") && !params.skip_smncopynumbercaller ) {
 
+        RENAME_BAM.out.output
+            .collect{it[1]}
+            .toList()
+            .set { ch_bam_list }
+
+        RENAME_BAI.out.output
+            .collect{it[1]}
+            .toList()
+            .set { ch_bai_list }
+
+        ch_case_info
+            .combine(ch_bam_list)
+            .combine(ch_bai_list)
+            .set { ch_bams_bais }
+
         SMNCOPYNUMBERCALLER (
             ch_bams_bais
         )