Fixed picard arg errors (280257df) · Commits · Chaos / Cutandrun

conf/modules.config

+2 −2

Original line number	Diff line number	Diff line
		@@ -331,7 +331,7 @@ if(params.run_q_filter) {
		if(params.run_mark_dups) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
		ext.args = "--ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
		ext.args = "ASSUME_SORT_ORDER=coordinate REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
		ext.prefix = { "${meta.id}.target.markdup" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		@@ -364,7 +364,7 @@ if(params.run_mark_dups) {
		if(params.run_remove_dups) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:PICARD_MARKDUPLICATES' {
		ext.args = "--ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
		ext.args = "ASSUME_SORT_ORDER=coordinate REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
		ext.prefix = { "${meta.id}.target.dedup" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },