Merge pull request #130 from luslab/dev (dbaad8c7) · Commits · Chaos / Cutandrun

modules/local/linux/cut.nf

+6 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ process CUT {

		output:
		tuple val(meta), path(".cut."), emit: file
		path "versions.yml" , emit: versions

		when:
		task.ext.when == null \|\| task.ext.when
		@@ -24,5 +25,10 @@ process CUT {

		"""
		cut $args $input $command > ${prefix}.cut.${ext}

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		cut: \$(cut --version \| head -n 1 \| awk '{print \$4;}')
		END_VERSIONS
		"""
		}

+6 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ process SORT {

		output:
		tuple val(meta), path(".sort."), emit: file
		path "versions.yml" , emit: versions

		when:
		task.ext.when == null \|\| task.ext.when
		@@ -26,5 +27,10 @@ process SORT {

		"""
		sort -T '.' $args $input_files > ${prefix}.sort.${ext}

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		sort: \$(sort --version \| head -n 1 \| awk '{print \$4;}')
		END_VERSIONS
		"""
		}

+1 −0

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@ workflow CONSENSUS_PEAKS {

		// Sort bed files
		SORT ( bed )
		ch_versions = ch_versions.mix(SORT.out.versions)

		// Merge peaks
		BEDTOOLS_MERGE ( SORT.out.file )

+4 −1

Original line number	Diff line number	Diff line
		@@ -653,9 +653,9 @@ workflow CUTANDRUN {
		AWK_FRAG_BIN(
		CALCULATE_FRAGMENTS.out.bed
		)
		ch_software_versions = ch_software_versions.mix(AWK_FRAG_BIN.out.versions)
		//AWK_FRAG_BIN.out.file \| view


		/*
		* CHANNEL: Combine bam and bai files on id
		*/
		@@ -765,6 +765,7 @@ workflow CUTANDRUN {
		ch_ordered_bigwig,
		ch_ordered_peaks_max_notempty
		)
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.versions)
		//EXAMPLE CHANNEL STRUCT: [[META], MATRIX]
		//DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.matrix \| view

		@@ -774,6 +775,7 @@ workflow CUTANDRUN {
		DEEPTOOLS_PLOTHEATMAP_PEAKS (
		DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.matrix
		)
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_PEAKS.out.versions)
		}

		/*
		@@ -817,6 +819,7 @@ workflow CUTANDRUN {
		CUT_CALC_REPROD (
		AWK_NAME_PEAK_BED.out.file
		)
		ch_software_versions = ch_software_versions.mix(CUT_CALC_REPROD.out.versions)

		/*
		* CHANNEL: Group samples based on group