diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..47ba54b66942c3d3e943b1133b9be1bace924edd --- /dev/null +++ b/src/nf_modules/picard/main.nf @@ -0,0 +1,27 @@ +version = "2.18.11" +container_url = "lbmc/picard:${version}" + +process mark_duplicate { + container = "${container_url}" + label "big_mem_mono_cpus" + tag "$file_id" + publishDir "results/mapping/ddup/", mode: 'copy' + + input: + tuple val(file_id), path(bam) + output: + tuple val(file_id) , path("*.bam"), emit: bam + path "*_report.txt", emit: report + + + script: +""" +PicardCommandLine MarkDuplicates \ + VALIDATION_STRINGENCY=LENIENT \ + REMOVE_DUPLICATES=true \ + INPUT=${bams[0]} \ + OUTPUT=${bams[0].baseName}_dedup.bam \ + METRICS_FILE=${bams[0].baseName}_picard_dedup_report.txt &> \ + picard_${bams[0].baseName}.log +""" +}