corrected versioning FASTQC_TRIMGALORE submodule (2983fec4) · Commits · Chaos / Cutandrun

subworkflows/local/fastqc_trimgalore.nf

+16 −16

Original line number	Diff line number	Diff line
		@@ -15,19 +15,19 @@ workflow FASTQC_TRIMGALORE {
		skip_trimming // boolean: true/false

		main:
		ch_versions = Channel.empty()

		fastqc_html = Channel.empty()
		fastqc_zip = Channel.empty()
		fastqc_versions = Channel.empty()
		if (!skip_fastqc) {
		FASTQC ( reads ).html.set { fastqc_html }
		fastqc_zip = FASTQC.out.zip
		fastqc_versions = FASTQC.out.versions
		ch_versions = ch_versions.mix(FASTQC.out.versions)
		}

		trim_html = Channel.empty()
		trim_zip = Channel.empty()
		trim_log = Channel.empty()
		trimgalore_versions = Channel.empty()
		ch_output_reads = reads
		if (!skip_trimming) {
		TRIMGALORE (
		@@ -37,18 +37,18 @@ workflow FASTQC_TRIMGALORE {
		trim_html = TRIMGALORE.out.html
		trim_zip = TRIMGALORE.out.zip
		trim_log = TRIMGALORE.out.log
		trimgalore_versions = TRIMGALORE.out.versions
		ch_versions = ch_versions.mix(TRIMGALORE.out.versions)

		}

		emit:
		reads = ch_output_reads // channel: [ val(meta), [ reads ] ]
		versions = ch_versions // channel: [ versions.yml ]

		fastqc_html // channel: [ val(meta), [ html ] ]
		fastqc_zip // channel: [ val(meta), [ zip ] ]
		fastqc_versions // path: *.version.txt

		trim_html // channel: [ val(meta), [ html ] ]
		trim_zip // channel: [ val(meta), [ zip ] ]
		trim_log // channel: [ val(meta), [ txt ] ]
		trimgalore_versions // path: *.version.txt
		}

+1 −2

Original line number	Diff line number	Diff line
		@@ -421,8 +421,7 @@ workflow CUTANDRUN {
		params.skip_trimming
		)
		ch_trimmed_reads = FASTQC_TRIMGALORE.out.reads
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.fastqc_versions)
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.trimgalore_versions)
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [READS]]
		//FASTQC_TRIMGALORE.out.reads \| view