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Merge pull request #400 from bjlang/dev
use subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer from nf-core/atacseq
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subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,155 @@ | ||
| // | ||
| // Call peaks with MACS2, annotate with HOMER and perform downstream QC | ||
| // | ||
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| include { MACS2_CALLPEAK } from '../../modules/nf-core/macs2/callpeak/main' | ||
| include { HOMER_ANNOTATEPEAKS } from '../../modules/nf-core/homer/annotatepeaks/main' | ||
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| include { FRIP_SCORE } from '../../modules/local/frip_score' | ||
| include { MULTIQC_CUSTOM_PEAKS } from '../../modules/local/multiqc_custom_peaks' | ||
| include { PLOT_MACS2_QC } from '../../modules/local/plot_macs2_qc' | ||
| include { PLOT_HOMER_ANNOTATEPEAKS } from '../../modules/local/plot_homer_annotatepeaks' | ||
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| workflow BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER { | ||
| take: | ||
| ch_bam // channel: [ val(meta), [ ip_bam ], [ control_bam ] ] | ||
| ch_fasta // channel: [ fasta ] | ||
| ch_gtf // channel: [ gtf ] | ||
| macs_gsize // integer: value for --macs_gsize parameter | ||
| annotate_peaks_suffix // string: suffix for input HOMER annotate peaks files to be trimmed off | ||
| ch_peak_count_header_multiqc // channel: [ header_file ] | ||
| ch_frip_score_multiqc // channel: [ header_file ] | ||
| ch_peak_annotation_header_multiqc // channel: [ header_file ] | ||
| is_narrow_peak // boolean: true/false | ||
| skip_peak_annotation // boolean: true/false | ||
| skip_peak_qc // boolean: true/false | ||
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| main: | ||
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| ch_versions = Channel.empty() | ||
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| // | ||
| // Call peaks with MACS2 | ||
| // | ||
| MACS2_CALLPEAK ( | ||
| ch_bam, | ||
| macs_gsize | ||
| ) | ||
| ch_versions = ch_versions.mix(MACS2_CALLPEAK.out.versions.first()) | ||
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| // | ||
| // Filter out samples with 0 MACS2 peaks called | ||
| // | ||
| MACS2_CALLPEAK | ||
| .out | ||
| .peak | ||
| .filter { | ||
| meta, peaks -> | ||
| peaks.size() > 0 | ||
| } | ||
| .set { ch_macs2_peaks } | ||
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| // Create channels: [ meta, ip_bam, peaks ] | ||
| ch_bam | ||
| .join(ch_macs2_peaks, by: [0]) | ||
| .map { | ||
| meta, ip_bam, control_bam, peaks -> | ||
| [ meta, ip_bam, peaks ] | ||
| } | ||
| .set { ch_bam_peaks } | ||
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| // | ||
| // Calculate FRiP score | ||
| // | ||
| FRIP_SCORE ( | ||
| ch_bam_peaks | ||
| ) | ||
| ch_versions = ch_versions.mix(FRIP_SCORE.out.versions.first()) | ||
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| // Create channels: [ meta, peaks, frip ] | ||
| ch_bam_peaks | ||
| .join(FRIP_SCORE.out.txt, by: [0]) | ||
| .map { | ||
| meta, ip_bam, peaks, frip -> | ||
| [ meta, peaks, frip ] | ||
| } | ||
| .set { ch_bam_peak_frip } | ||
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| // | ||
| // FRiP score custom content for MultiQC | ||
| // | ||
| MULTIQC_CUSTOM_PEAKS ( | ||
| ch_bam_peak_frip, | ||
| ch_peak_count_header_multiqc, | ||
| ch_frip_score_multiqc | ||
| ) | ||
| ch_versions = ch_versions.mix(MULTIQC_CUSTOM_PEAKS.out.versions.first()) | ||
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| ch_homer_annotatepeaks = Channel.empty() | ||
| ch_plot_macs2_qc_txt = Channel.empty() | ||
| ch_plot_macs2_qc_pdf = Channel.empty() | ||
| ch_plot_homer_annotatepeaks_txt = Channel.empty() | ||
| ch_plot_homer_annotatepeaks_pdf = Channel.empty() | ||
| ch_plot_homer_annotatepeaks_tsv = Channel.empty() | ||
| if (!skip_peak_annotation) { | ||
| // | ||
| // Annotate peaks with HOMER | ||
| // | ||
| HOMER_ANNOTATEPEAKS ( | ||
| ch_macs2_peaks, | ||
| ch_fasta, | ||
| ch_gtf | ||
| ) | ||
| ch_homer_annotatepeaks = HOMER_ANNOTATEPEAKS.out.txt | ||
| ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS.out.versions.first()) | ||
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| if (!skip_peak_qc) { | ||
| // | ||
| // MACS2 QC plots with R | ||
| // | ||
| PLOT_MACS2_QC ( | ||
| ch_macs2_peaks.collect{it[1]}, | ||
| is_narrow_peak | ||
| ) | ||
| ch_plot_macs2_qc_txt = PLOT_MACS2_QC.out.txt | ||
| ch_plot_macs2_qc_pdf = PLOT_MACS2_QC.out.pdf | ||
| ch_versions = ch_versions.mix(PLOT_MACS2_QC.out.versions) | ||
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| // | ||
| // Peak annotation QC plots with R | ||
| // | ||
| PLOT_HOMER_ANNOTATEPEAKS ( | ||
| HOMER_ANNOTATEPEAKS.out.txt.collect{it[1]}, | ||
| ch_peak_annotation_header_multiqc, | ||
| annotate_peaks_suffix | ||
| ) | ||
| ch_plot_homer_annotatepeaks_txt = PLOT_HOMER_ANNOTATEPEAKS.out.txt | ||
| ch_plot_homer_annotatepeaks_pdf = PLOT_HOMER_ANNOTATEPEAKS.out.pdf | ||
| ch_plot_homer_annotatepeaks_tsv = PLOT_HOMER_ANNOTATEPEAKS.out.tsv | ||
| ch_versions = ch_versions.mix(PLOT_HOMER_ANNOTATEPEAKS.out.versions) | ||
| } | ||
| } | ||
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| emit: | ||
| peaks = ch_macs2_peaks // channel: [ val(meta), [ peaks ] ] | ||
| xls = MACS2_CALLPEAK.out.xls // channel: [ val(meta), [ xls ] ] | ||
| gapped_peaks = MACS2_CALLPEAK.out.gapped // channel: [ val(meta), [ gapped_peak ] ] | ||
| bed = MACS2_CALLPEAK.out.bed // channel: [ val(meta), [ bed ] ] | ||
| bedgraph = MACS2_CALLPEAK.out.bdg // channel: [ val(meta), [ bedgraph ] ] | ||
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| frip_txt = FRIP_SCORE.out.txt // channel: [ val(meta), [ txt ] ] | ||
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| frip_multiqc = MULTIQC_CUSTOM_PEAKS.out.frip // channel: [ val(meta), [ frip ] ] | ||
| peak_count_multiqc = MULTIQC_CUSTOM_PEAKS.out.count // channel: [ val(meta), [ counts ] ] | ||
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| homer_annotatepeaks = ch_homer_annotatepeaks // channel: [ val(meta), [ txt ] ] | ||
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| plot_macs2_qc_txt = ch_plot_macs2_qc_txt // channel: [ txt ] | ||
| plot_macs2_qc_pdf = ch_plot_macs2_qc_pdf // channel: [ pdf ] | ||
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| plot_homer_annotatepeaks_txt = ch_plot_homer_annotatepeaks_txt // channel: [ txt ] | ||
| plot_homer_annotatepeaks_pdf = ch_plot_homer_annotatepeaks_pdf // channel: [ pdf ] | ||
| plot_homer_annotatepeaks_tsv = ch_plot_homer_annotatepeaks_tsv // channel: [ tsv ] | ||
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| versions = ch_versions // channel: [ versions.yml ] | ||
| } |
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