diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf index 42cd607780a4118491e4612e74cdeb93f032fc5a..67ab922755786b7856c7df2922eb7a0c166ea457 100644 --- a/src/nf_modules/bwa/main.nf +++ b/src/nf_modules/bwa/main.nf @@ -38,7 +38,7 @@ process mapping_fastq { script: """ bwa mem -t ${task.cpus} \ --R ${bwa_mem_R} \ +-R ${params.bwa_mem_R} \ ${index_id} ${reads[0]} ${reads[1]} 2> \ ${file_id}_bwa_report.txt | \ samtools view -@ ${task.cpus} -Sb - > ${file_id}.bam