Merge pull request #44 from luslab/dev (880a0793) · Commits · Chaos / Cutandrun

workflows/cutandrun.nf

+18 −18

Original line number	Diff line number	Diff line
		@@ -143,12 +143,12 @@ if(params.only_filtering) {
		run_remove_dups = false
		run_peak_calling = false
		run_reporting = false
		run_multiqc = false
		run_multiqc = true
		}

		if(params.only_peak_calling) {
		run_reporting = false
		run_multiqc = false
		run_multiqc = true
		}

		/*
		@@ -350,6 +350,7 @@ workflow CUTANDRUN {

		// Init
		ch_software_versions = Channel.empty()
		ch_frag_len_multiqc = Channel.empty()

		/*
		* SUBWORKFLOW: Uncompress and prepare reference genome files
		@@ -920,7 +921,6 @@ workflow CUTANDRUN {
		/*
		* MODULE: Generate python reporting using mixture of meta-data and direct file processing
		*/
		ch_frag_len_multiqc = Channel.empty()
		GENERATE_REPORTS(
		EXPORT_META.out.csv, // meta-data report stats
		SAMTOOLS_CUSTOMVIEW.out.tsv.collect{it[1]}, // raw fragments
		@@ -932,6 +932,7 @@ workflow CUTANDRUN {
		)
		ch_frag_len_multiqc = GENERATE_REPORTS.out.frag_len_multiqc
		ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.version.ifEmpty(null))
		}

		/*
		* MODULE: Collect software versions used in pipeline
		@@ -947,7 +948,6 @@ workflow CUTANDRUN {
		GET_SOFTWARE_VERSIONS (
		ch_software_versions.map { it }.collect()
		)
		}

		/*
		* MODULE: Multiqc