Merge pull request nf-core#592 from MaxUlysse/Header

Add custom CN field in BAM files

Author: Szilveszter Juhos

configuration/base.config

@@ -38,6 +38,7 @@ params {
   repository = wf_repository // DockerHub containers repository
   sample = '' // sample files in tsv format
   sampleDir = '' // samples directory (for Germline only)
+  sequencing_center = '' // CN field in BAM files
   singularity = false // Don't use singularity to build buildContainers.nf
   step = 'mapping' // Default step is mapping
   strelkaBP = false // Don't use Manta's candidate indels as input to Strelka

lib/SarekUtils.groovy

@@ -51,6 +51,7 @@ class MyUtils {
       'sample-dir',
       'sample',
       'sampleDir',
+      'sequencing_center',
       'single-CPUMem',
       'singleCPUMem',
       'singularity',

main.nf

@@ -176,7 +176,8 @@ process MapReads {
   when: step == 'mapping' && !params.onlyQC
 
   script:
-  readGroup = "@RG\\tID:${idRun}\\tPU:${idRun}\\tSM:${idSample}\\tLB:${idSample}\\tPL:illumina"
+  CN = params.sequencing_center ? "CN:${params.sequencing_center}\\t" : ""
+  readGroup = "@RG\\tID:${idRun}\\t${CN}PU:${idRun}\\tSM:${idSample}\\tLB:${idSample}\\tPL:illumina"
   // adjust mismatch penalty for tumor samples
   extra = status == 1 ? "-B 3" : ""
   """