corrected versioning for ANNOTATE_META_AWK subworkflow (38df60cd) · Commits · Chaos / Cutandrun

subworkflows/local/annotate_meta_awk.nf

+7 −1

Original line number	Diff line number	Diff line
		@@ -18,6 +18,8 @@ workflow ANNOTATE_META_AWK {
		script

		main:
		ch_versions = Channel.empty()

		// Strip out the sample id from the meta in the passthrough
		ch_paths = passthrough.map { row -> [row[0].id, row[0], row[1..-1]].flatten() }

		@@ -25,6 +27,7 @@ workflow ANNOTATE_META_AWK {
		// Can run awk in script mode with a file from assets or with a setup of command line args
		if(params.script_mode) {
		AWK_SCRIPT ( report, script )
		ch_versions = ch_versions.mix(AWK_SCRIPT.out.versions)

		AWK_SCRIPT.out.file
		.splitCsv(header:true)
		@@ -39,6 +42,7 @@ workflow ANNOTATE_META_AWK {
		}
		else {
		AWK ( report )
		ch_versions = ch_versions.mix(AWK.out.versions)

		AWK.out.file
		.splitCsv(header:true)
		@@ -54,4 +58,6 @@ workflow ANNOTATE_META_AWK {

		emit:
		output = ch_annotated_meta // channel: [ val(annotated_meta), [ passthrough ] ]
		versions = ch_versions // channel: [ versions.yml ]

		}

+7 −2

Original line number	Diff line number	Diff line
		@@ -538,6 +538,7 @@ workflow CUTANDRUN {
		ch_bowtie2_log,
		ch_bt2_to_csv_awk
		)
		ch_software_versions = ch_software_versions.mix(ANNOTATE_BT2_META.out.versions)

		ANNOTATE_BT2_SPIKEIN_META (
		ANNOTATE_BT2_META.out.output,
		@@ -545,6 +546,8 @@ workflow CUTANDRUN {
		ch_bt2_to_csv_awk
		)
		ch_samtools_bam = ANNOTATE_BT2_SPIKEIN_META.out.output
		ch_software_versions = ch_software_versions.mix(ANNOTATE_BT2_META.out.versions)

		}
		// META-DATA example state:
		//[[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false,
		@@ -563,6 +566,8 @@ workflow CUTANDRUN {
		ch_dummy_file.collect()
		)
		ch_samtools_bam = ANNOTATE_DEDUP_META.out.output
		ch_software_versions = ch_software_versions.mix(ANNOTATE_DEDUP_META.out.versions)

		}
		//EXAMPLE CHANNEL STRUCT: [[META + dedup_library:unknown library, dedup_unpaired_reads_examined:0, dedup_read_pairs_examined:350, dedup_secondary_or_supplementary_rds:0,
		// dedup_unmapped_reads:0, dedup_unpaired_read_duplicates:0, dedup_read_pair_duplicates:0, dedup_read_pair_optical_duplicates:0, dedup_percent_duplication:0,

+2 −2

File changed.

Contains only whitespace changes.