Merge pull request #522 from genomic-medicine-sweden/smncopynumber-up…

…date

Fix samplenames in smncopynumbercaller

modules/local/rename_align_files.nf

@@ -0,0 +1,30 @@
+process RENAME_ALIGN_FILES {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "conda-forge::coreutils=8.31"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--0' :
+        'biocontainers/gnu-wget:1.18--0' }"
+
+    input:
+    tuple val(meta), path(input)
+    val(extension)
+
+    output:
+    path("*.{bam,bai}"), emit: output
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    ln -s $input ${meta.sample}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ln: \$(echo \$(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
+    END_VERSIONS
+    """
+}

workflows/raredisease.nf

@@ -101,9 +101,16 @@ if (missingParamsCount>0) {
 // MODULE: Installed directly from nf-core/modules
 //
 
-include { FASTQC                                } from '../modules/nf-core/fastqc/main'
-include { MULTIQC                               } from '../modules/nf-core/multiqc/main'
-include { SMNCOPYNUMBERCALLER                   } from '../modules/nf-core/smncopynumbercaller/main'
+include { FASTQC              } from '../modules/nf-core/fastqc/main'
+include { MULTIQC             } from '../modules/nf-core/multiqc/main'
+include { SMNCOPYNUMBERCALLER } from '../modules/nf-core/smncopynumbercaller/main'
+
+//
+// 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'
 
 //
 // SUBWORKFLOWS
@@ -578,13 +585,13 @@ workflow RAREDISEASE {
     }
 
     // STEP 1.7: SMNCOPYNUMBERCALLER
-    ch_mapped.genome_bam_bai
-        .collect{it[1]}
+    RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
+        .collect{it}
         .toList()
         .set { ch_bam_list }
 
-    ch_mapped.genome_bam_bai
-        .collect{it[2]}
+    RENAME_BAI_FOR_SMNCALLER(ch_mapped.genome_marked_bai, "bam.bai").output
+        .collect{it}
         .toList()
         .set { ch_bai_list }
 
@@ -596,6 +603,8 @@ 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(SMNCOPYNUMBERCALLER.out.versions)
 
     // ped correspondence, sex check, ancestry check