Pass read group fields to bowtie2

Author: JoseEspinosa

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #392](https://github.com/nf-core/chipseq/pull/392)] - Adding line numbers to warnings/errors messages in `bin/check_samplesheet.py`.
 - [[#396](https://github.com/nf-core/chipseq/issues/396)] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores.
 - [[#378](https://github.com/nf-core/chipseq/issues/378)] - Switch from macs2 to macs3.
+- [[#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2.
 
 ### Software dependencies
 

conf/modules.config

@@ -225,7 +225,12 @@ if (params.aligner == 'bwa') {
 if (params.aligner == 'bowtie2') {
     process {
         withName: 'BOWTIE2_ALIGN' {
-            ext.args   = ''
+            ext.args   = {
+                [
+                    meta.read_group ? "--rg-id ${meta.id} --rg SM:${meta.id - ~/_T\d+$/} --rg PL:ILLUMINA --rg LB:${meta.id} --rg PU:1" : '',
+                    params.seq_center ? "--rg CN:${params.seq_center}" : ''
+                ].join(' ').trim()
+            }
             ext.prefix = { "${meta.id}.Lb" }
             publishDir = [
                 [

subworkflows/local/input_check.nf

@@ -29,9 +29,9 @@ def create_fastq_channel(LinkedHashMap row, String seq_center) {
     meta.antibody   = row.antibody
     meta.control    = row.control
 
-    def read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id.split('_')[0..-2].join('_')}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\'"
+    def read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\'"
     if (seq_center) {
-        read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id.split('_')[0..-2].join('_')}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\\tCN:${seq_center}\'"
+        read_group = "\'@RG\\tID:${meta.id}\\tSM:${meta.id - ~/_T\d+$/}\\tPL:ILLUMINA\\tLB:${meta.id}\\tPU:1\\tCN:${seq_center}\'"
     }
     meta.read_group = read_group