diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf index 785201c76fff893dc28697b07940e83fc4179e83..7d2abd12c697b14f4ac076f078c7cf8407c1b6b5 100644 --- a/src/nf_modules/bwa/main.nf +++ b/src/nf_modules/bwa/main.nf @@ -43,7 +43,7 @@ if (file_id.containsKey('library')) { bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumina" """ bwa mem -t ${task.cpus} \ --R '${params.bwa_mem_R}' \ +-R '${bwa_mem_R}' \ ${index_id} ${reads[0]} ${reads[1]} 2> \ ${file_id}_bwa_report.txt | \ samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam