changed version storage in cutandrun.nf (38253b4b) · Commits · Chaos / Cutandrun

workflows/cutandrun.nf

+10 −10

Original line number	Diff line number	Diff line
		@@ -421,8 +421,8 @@ workflow CUTANDRUN {
		params.skip_trimming
		)
		ch_trimmed_reads = FASTQC_TRIMGALORE.out.reads
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.fastqc_versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.trimgalore_versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.fastqc_versions)
		ch_software_versions = ch_software_versions.mix(FASTQC_TRIMGALORE.out.trimgalore_versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [READS]]
		//FASTQC_TRIMGALORE.out.reads \| view
		@@ -452,7 +452,7 @@ workflow CUTANDRUN {
		PREPARE_GENOME.out.bowtie2_index,
		PREPARE_GENOME.out.bowtie2_spikein_index
		)
		ch_software_versions = ch_software_versions.mix(ALIGN_BOWTIE2.out.bowtie2_versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(ALIGN_BOWTIE2.out.bowtie2_versions)
		ch_orig_bam = ALIGN_BOWTIE2.out.orig_bam
		ch_orig_spikein_bam = ALIGN_BOWTIE2.out.orig_spikein_bam
		ch_bowtie2_log = ALIGN_BOWTIE2.out.bowtie2_log
		@@ -505,7 +505,7 @@ workflow CUTANDRUN {
		ch_samtools_flagstat = MARK_DUPLICATES_PICARD.out.flagstat
		ch_samtools_idxstats = MARK_DUPLICATES_PICARD.out.idxstats
		ch_markduplicates_metrics = MARK_DUPLICATES_PICARD.out.metrics
		ch_software_versions = ch_software_versions.mix(MARK_DUPLICATES_PICARD.out.picard_versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(MARK_DUPLICATES_PICARD.out.picard_versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//ch_samtools_bam \| view
		@@ -640,7 +640,7 @@ workflow CUTANDRUN {
		UCSC_BEDCLIP.out.bedgraph,
		PREPARE_GENOME.out.chrom_sizes
		)
		ch_software_versions = ch_software_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions)
		//EXAMPLE CHANNEL STRUCT: [[META], BIGWIG]
		//UCSC_BEDGRAPHTOBIGWIG.out.bigwig \| view

		@@ -692,7 +692,7 @@ workflow CUTANDRUN {
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK.out.bed
		//ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions.first().ifEmpty(null))
		//ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_CALLPEAK.out.bed \| view
		}
		@@ -714,7 +714,7 @@ workflow CUTANDRUN {
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK_NOIGG.out.bed
		//ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.version.first().ifEmpty(null))
		//ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_NO_IGG.out.bed \| view
		}
		@@ -801,7 +801,7 @@ workflow CUTANDRUN {
		CALCULATE_FRAGMENTS (
		ch_samtools_bam
		)
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRAGMENTS.out.bedtools_versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRAGMENTS.out.bedtools_versions)
		//EXAMPLE CHANNEL STRUCT: NO CHANGE
		//CALCULATE_FRAGMENTS.out.bed \| view

		@@ -898,7 +898,7 @@ workflow CUTANDRUN {
		ch_bigwig_no_igg,
		PREPARE_GENOME.out.bed
		)
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_GENE.out.versions.first().ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_GENE.out.versions)

		/*
		* MODULE: Calculate DeepTools heatmap
		@@ -1030,7 +1030,7 @@ workflow CUTANDRUN {
		ch_frag_len_header_multiqc // multiqc config header for fragment length distribution plot
		)
		ch_frag_len_multiqc = GENERATE_REPORTS.out.frag_len_multiqc
		ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.versions.ifEmpty(null))
		ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.versions)
		}

		/*

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