diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf index 8f395a605cd793a4fba1bfb9636034985b31791d..42cd607780a4118491e4612e74cdeb93f032fc5a 100644 --- a/src/nf_modules/bwa/main.nf +++ b/src/nf_modules/bwa/main.nf @@ -21,6 +21,7 @@ bwa index -p ${fasta.simpleName} ${fasta} \ } +params.bwa_mem_R = '@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina' process mapping_fastq { container = "${container_url}" label "big_mem_multi_cpus" @@ -37,6 +38,7 @@ process mapping_fastq { script: """ bwa mem -t ${task.cpus} \ +-R ${bwa_mem_R} \ ${index_id} ${reads[0]} ${reads[1]} 2> \ ${file_id}_bwa_report.txt | \ samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam