syntax fix (8b64b8ed) · Commits · Chaos / Cutandrun

workflows/cutandrun.nf

+7 −3

Original line number	Diff line number	Diff line
		@@ -378,6 +378,7 @@ workflow CUTANDRUN {
		INPUT_CHECK (
		ch_input
		)
		ch_software_versions = ch_software_versions.mix(INPUT_CHECK.out.versions)

		INPUT_CHECK.out.reads
		.map {
		@@ -402,6 +403,7 @@ workflow CUTANDRUN {
		CAT_FASTQ (
		ch_fastq.multiple
		)
		ch_software_versions = ch_software_versions.mix(CAT_FASTQ.out.versions)

		CAT_FASTQ.out.reads
		.mix(ch_fastq.single)
		@@ -485,6 +487,7 @@ workflow CUTANDRUN {
		ch_samtools_stats = SAMTOOLS_VIEW_SORT_STATS.out.stats
		ch_samtools_flagstat = SAMTOOLS_VIEW_SORT_STATS.out.flagstat
		ch_samtools_idxstats = SAMTOOLS_VIEW_SORT_STATS.out.idxstats
		ch_software_versions = ch_software_versions.mix(SAMTOOLS_VIEW_SORT_STATS.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//ch_samtools_bam \| view
		@@ -545,8 +548,6 @@ 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_SPIKEIN_META.out.versions)

		}
		// META-DATA example state:
		//[[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false,
		@@ -624,6 +625,7 @@ workflow CUTANDRUN {
		BEDTOOLS_GENOMECOV_SCALE (
		ch_samtools_bam_scale
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_GENOMECOV_SCALE.out.versions)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//BEDTOOLS_GENOMECOV_SCALE.out.bedgraph \| view

		@@ -634,6 +636,7 @@ workflow CUTANDRUN {
		BEDTOOLS_GENOMECOV_SCALE.out.bedgraph,
		PREPARE_GENOME.out.chrom_sizes
		)
		ch_software_versions = ch_software_versions.mix(UCSC_BEDCLIP.out.versions)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//UCSC_BEDCLIP.out.bedgraph \| view

		@@ -696,6 +699,7 @@ workflow CUTANDRUN {
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		//ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_CALLPEAK.out.bed \| view

modules/local/linux/awk.nf

+1 −1

File changed.

Contains only whitespace changes.

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