Syntax and comments fix (6d7d3d0c) · Commits · Chaos / Cutandrun

bin/check_samplesheet.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -155,7 +155,7 @@ def check_samplesheet(file_in, file_out, igg_control):
		else:
		sample_run_dict[sample][replicate].append(sample_info)

		## Store unique group names
		## Store unique sample names
		if sample not in sample_names_list:
		sample_names_list.append(sample)

workflows/cutandrun.nf

+14 −14

Original line number	Diff line number	Diff line
		@@ -215,7 +215,7 @@ workflow CUTANDRUN {
		.mix(ch_fastq.single)
		.set { ch_cat_fastq }
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [READS]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [READS]]
		//ch_cat_fastq \| view

		/*
		@@ -230,7 +230,7 @@ workflow CUTANDRUN {
		ch_trimmed_reads = FASTQC_TRIMGALORE.out.reads
		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]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [READS]]
		//FASTQC_TRIMGALORE.out.reads \| view

		/*
		@@ -276,7 +276,7 @@ workflow CUTANDRUN {
		ch_samtools_spikein_idxstats = ALIGN_BOWTIE2.out.spikein_idxstats
		}
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
		// ch_samtools_bam \| view

		/*
		@@ -294,7 +294,7 @@ workflow CUTANDRUN {
		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]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
		//ch_samtools_bam \| view

		/*
		@@ -314,7 +314,7 @@ workflow CUTANDRUN {
		ch_markduplicates_metrics = MARK_DUPLICATES_PICARD.out.metrics
		ch_software_versions = ch_software_versions.mix(MARK_DUPLICATES_PICARD.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
		//ch_samtools_bam \| view

		/*
		@@ -334,7 +334,7 @@ workflow CUTANDRUN {
		ch_dedup_multiqc = DEDUPLICATE_PICARD.out.metrics
		ch_software_versions = ch_software_versions.mix(DEDUPLICATE_PICARD.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false], [BAM]]
		//ch_samtools_bam \| view

		/*
		@@ -363,7 +363,7 @@ workflow CUTANDRUN {
		ch_samtools_bam = ANNOTATE_BT2_SPIKEIN_META.out.output
		}
		// META-DATA example state:
		//[[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false,
		//[[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false, is_control:false,
		// bt2_total_reads_spikein:9616, bt2_align1_spikein:1, bt2_align_gt1_spikein:0, bt2_non_aligned_spikein:9615, bt2_total_aligned_spikein:1,
		// bt2_total_reads_target:9616, bt2_align1_target:315, bt2_align_gt1_target:449, bt2_non_aligned_target:8852, bt2_total_aligned_target:764], BAM]
		//ch_samtools_bam \| view
		@@ -411,8 +411,8 @@ workflow CUTANDRUN {
		* CHANNEL: Separate bedgraphs into target/control
		*/
		ch_bedgraph.branch { it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		target: it[0].is_control != 1
		control: it[0].is_control == 1
		}
		.set { ch_bedgraph_split }
		//ch_bedgraph_split.target \| view
		@@ -465,8 +465,8 @@ workflow CUTANDRUN {

		if('macs2' in callers) {
		ch_samtools_bam.branch{ it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		target: it[0].is_control != 1
		control: it[0].is_control == 1
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view
		@@ -532,8 +532,8 @@ workflow CUTANDRUN {

		if('macs2' in callers) {
		ch_samtools_bam.branch{ it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		target: it[0].is_control != 1
		control: it[0].is_control == 1
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view
		@@ -724,7 +724,7 @@ workflow CUTANDRUN {
		* CHANNEL: Remove IgG from bigwig channel
		*/
		ch_bigwig
		.filter { it[0].group != "igg" }
		.filter { it[0].is_control != 1 }
		.set { ch_bigwig_no_igg }
		//ch_bigwig_no_igg \| view

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