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Merge pull request #401 from bjlang/dev
create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq
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subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,158 @@ | ||
| // | ||
| // Call consensus peaks with BEDTools and custom scripts, annotate with HOMER, quantify with featureCounts and QC with DESeq2 | ||
| // | ||
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| include { HOMER_ANNOTATEPEAKS } from '../../modules/nf-core/homer/annotatepeaks/main' | ||
| include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts/main' | ||
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| include { MACS2_CONSENSUS } from '../../modules/local/macs2_consensus' | ||
| include { ANNOTATE_BOOLEAN_PEAKS } from '../../modules/local/annotate_boolean_peaks' | ||
| include { DESEQ2_QC } from '../../modules/local/deseq2_qc' | ||
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| workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 { | ||
| take: | ||
| ch_peaks // channel: [ val(meta), [ peaks ] ] | ||
| ch_bams // channel: [ val(meta), [ ip_bams ] ] | ||
| ch_fasta // channel: [ fasta ] | ||
| ch_gtf // channel: [ gtf ] | ||
| ch_deseq2_pca_header_multiqc // channel: [ header_file ] | ||
| ch_deseq2_clustering_header_multiqc // channel: [ header_file ] | ||
| is_narrow_peak // boolean: true/false | ||
| skip_peak_annotation // boolean: true/false | ||
| skip_deseq2_qc // boolean: true/false | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| // Create channels: [ meta , [ peaks ] ] | ||
| // Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ] | ||
| ch_peaks | ||
| .map { | ||
| meta, peak -> | ||
| [ meta.antibody, meta.id.split('_')[0..-2].join('_'), peak ] | ||
| } | ||
| .groupTuple() | ||
| .map { | ||
| antibody, groups, peaks -> | ||
| [ | ||
| antibody, | ||
| groups.groupBy().collectEntries { [(it.key) : it.value.size()] }, | ||
| peaks | ||
| ] | ||
| } | ||
| .map { | ||
| antibody, groups, peaks -> | ||
| def meta_new = [:] | ||
| meta_new.id = antibody | ||
| meta_new.multiple_groups = groups.size() > 1 | ||
| meta_new.replicates_exist = groups.max { groups.value }.value > 1 | ||
| [ meta_new, peaks ] | ||
| } | ||
| .set { ch_antibody_peaks } | ||
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| // | ||
| // Generate consensus peaks across samples | ||
| // | ||
| MACS2_CONSENSUS ( | ||
| ch_antibody_peaks, | ||
| is_narrow_peak | ||
| ) | ||
| ch_versions = ch_versions.mix(MACS2_CONSENSUS.out.versions) | ||
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| // | ||
| // Annotate consensus peaks | ||
| // | ||
| if (!skip_peak_annotation) { | ||
| HOMER_ANNOTATEPEAKS ( | ||
| MACS2_CONSENSUS.out.bed, | ||
| ch_fasta, | ||
| ch_gtf | ||
| ) | ||
| ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions) | ||
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| // | ||
| // MODULE: Add boolean fields to annotated consensus peaks to aid filtering | ||
| // | ||
| ANNOTATE_BOOLEAN_PEAKS ( | ||
| MACS2_CONSENSUS.out.boolean_txt.join(HOMER_ANNOTATEPEAKS.out.txt, by: [0]), | ||
| ) | ||
| ch_versions = ch_versions.mix(ANNOTATE_BOOLEAN_PEAKS.out.versions) | ||
| } | ||
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| // Create channels: [ meta, [ ip_bams ], saf ] | ||
| MACS2_CONSENSUS | ||
| .out | ||
| .saf | ||
| .map { | ||
| meta, saf -> | ||
| [ meta.id, meta, saf ] | ||
| } | ||
| .join(ch_bams) | ||
| .map { | ||
| antibody, meta, saf, bams -> | ||
| [ meta, bams.flatten().sort(), saf ] | ||
| } | ||
| .set { ch_bam_saf } | ||
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| // | ||
| // Quantify peaks across samples with featureCounts | ||
| // | ||
| SUBREAD_FEATURECOUNTS ( | ||
| ch_bam_saf | ||
| ) | ||
| ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions) | ||
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| // | ||
| // Generate QC plots with DESeq2 | ||
| // | ||
| ch_deseq2_qc_pdf = Channel.empty() | ||
| ch_deseq2_qc_rdata = Channel.empty() | ||
| ch_deseq2_qc_rds = Channel.empty() | ||
| ch_deseq2_qc_pca_txt = Channel.empty() | ||
| ch_deseq2_qc_pca_multiqc = Channel.empty() | ||
| ch_deseq2_qc_dists_txt = Channel.empty() | ||
| ch_deseq2_qc_dists_multiqc = Channel.empty() | ||
| ch_deseq2_qc_log = Channel.empty() | ||
| ch_deseq2_qc_size_factors = Channel.empty() | ||
| if (!skip_deseq2_qc) { | ||
| DESEQ2_QC ( | ||
| SUBREAD_FEATURECOUNTS.out.counts, | ||
| ch_deseq2_pca_header_multiqc, | ||
| ch_deseq2_clustering_header_multiqc | ||
| ) | ||
| ch_deseq2_qc_pdf = DESEQ2_QC.out.pdf | ||
| ch_deseq2_qc_rdata = DESEQ2_QC.out.rdata | ||
| ch_deseq2_qc_rds = DESEQ2_QC.out.rds | ||
| ch_deseq2_qc_pca_txt = DESEQ2_QC.out.pca_txt | ||
| ch_deseq2_qc_pca_multiqc = DESEQ2_QC.out.pca_multiqc | ||
| ch_deseq2_qc_dists_txt = DESEQ2_QC.out.dists_txt | ||
| ch_deseq2_qc_dists_multiqc = DESEQ2_QC.out.dists_multiqc | ||
| ch_deseq2_qc_log = DESEQ2_QC.out.log | ||
| ch_deseq2_qc_size_factors = DESEQ2_QC.out.size_factors | ||
| ch_versions = ch_versions.mix(DESEQ2_QC.out.versions) | ||
| } | ||
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| emit: | ||
| consensus_bed = MACS2_CONSENSUS.out.bed // channel: [ bed ] | ||
| consensus_saf = MACS2_CONSENSUS.out.saf // channel: [ saf ] | ||
| consensus_pdf = MACS2_CONSENSUS.out.pdf // channel: [ pdf ] | ||
| consensus_txt = MACS2_CONSENSUS.out.txt // channel: [ pdf ] | ||
| consensus_boolean_txt = MACS2_CONSENSUS.out.boolean_txt // channel: [ txt ] | ||
| consensus_intersect_txt = MACS2_CONSENSUS.out.intersect_txt // channel: [ txt ] | ||
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| featurecounts_txt = SUBREAD_FEATURECOUNTS.out.counts // channel: [ txt ] | ||
| featurecounts_summary = SUBREAD_FEATURECOUNTS.out.summary // channel: [ txt ] | ||
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| deseq2_qc_pdf = ch_deseq2_qc_pdf // channel: [ pdf ] | ||
| deseq2_qc_rdata = ch_deseq2_qc_rdata // channel: [ rdata ] | ||
| deseq2_qc_rds = ch_deseq2_qc_rds // channel: [ rds ] | ||
| deseq2_qc_pca_txt = ch_deseq2_qc_pca_txt // channel: [ txt ] | ||
| deseq2_qc_pca_multiqc = ch_deseq2_qc_pca_multiqc // channel: [ txt ] | ||
| deseq2_qc_dists_txt = ch_deseq2_qc_dists_txt // channel: [ txt ] | ||
| deseq2_qc_dists_multiqc = ch_deseq2_qc_dists_multiqc // channel: [ txt ] | ||
| deseq2_qc_log = ch_deseq2_qc_log // channel: [ txt ] | ||
| deseq2_qc_size_factors = ch_deseq2_qc_size_factors // channel: [ txt ] | ||
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| versions = ch_versions // channel: [ versions.yml ] | ||
| } |
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