diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf index 7e2efd4f44933ab1d0b0c9612a6400ea35c80173..4f197fbd46d09b98491aa14f45d77e0804853f3a 100644 --- a/src/nf_modules/samtools/main.nf +++ b/src/nf_modules/samtools/main.nf @@ -123,3 +123,20 @@ process merge_bam { samtools merge ${first_bam} ${second_bam} ${first_bam_id}_${second_file_id}.bam """ } + +process bam_stats { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$file_id" + cpus = 2 + + input: + tuple val(file_id), path(bam) + + output: + tuple val(file_id), path("*.tsv"), emit: tsv + script: +""" +samtools flagstat -O tsv ${bam} > ${file_id}.tsv +""" +}