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create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq #401

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merged 3 commits into from
Jul 9, 2024
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create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer similar to nf-core/atacseq #401

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bb76db7
create subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer simi…
Jul 8, 2024
132892e
fix includes
Jul 8, 2024
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suggestions from code review
Jul 9, 2024
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14 changes: 7 additions & 7 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -540,7 +540,7 @@ if (!params.skip_plot_fingerprint) {
}

process {
withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:MACS2_CALLPEAK' {
withName: 'MACS2_CALLPEAK' {
ext.args = [
'--keep-dup all',
params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
Expand All @@ -559,15 +559,15 @@ process {
]
}

withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:FRIP_SCORE' {
withName: 'FRIP_SCORE' {
ext.args = '-bed -c -f 0.20'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
enabled: false
]
}

withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:MULTIQC_CUSTOM_PEAKS' {
withName: 'MULTIQC_CUSTOM_PEAKS' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
mode: params.publish_dir_mode,
Expand All @@ -591,7 +591,7 @@ if (!params.skip_peak_annotation) {

if (!params.skip_peak_qc) {
process {
withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:PLOT_MACS2_QC' {
withName: 'PLOT_MACS2_QC' {
ext.args = '-o ./ -p macs2_peak'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
Expand All @@ -600,7 +600,7 @@ if (!params.skip_peak_annotation) {
]
}

withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER:PLOT_HOMER_ANNOTATEPEAKS' {
withName: 'PLOT_HOMER_ANNOTATEPEAKS' {
ext.args = '-o ./'
ext.prefix = 'macs2_annotatePeaks'
publishDir = [
Expand Down Expand Up @@ -638,7 +638,7 @@ if (!params.skip_consensus_peaks) {

if (!params.skip_peak_annotation) {
process {
withName: 'HOMER_ANNOTATEPEAKS_CONSENSUS' {
withName: '.*:BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2:HOMER_ANNOTATEPEAKS' {
ext.args = '-gid'
ext.prefix = { "${meta.id}.consensus_peaks" }
publishDir = [
Expand All @@ -661,7 +661,7 @@ if (!params.skip_consensus_peaks) {

if (!params.skip_deseq2_qc) {
process {
withName: DESEQ2_QC {
withName: 'DESEQ2_QC' {
ext.when = { meta.multiple_groups && meta.replicates_exist }
ext.args = [
'--id_col 1',
Expand Down
158 changes: 158 additions & 0 deletions subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,158 @@
//
// Call consensus peaks with BEDTools and custom scripts, annotate with HOMER, quantify with featureCounts and QC with DESeq2
//

include { HOMER_ANNOTATEPEAKS } from '../../modules/nf-core/homer/annotatepeaks/main'
include { SUBREAD_FEATURECOUNTS } from '../../modules/nf-core/subread/featurecounts/main'

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'

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

main:

ch_versions = Channel.empty()

// 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 }

//
// Generate consensus peaks across samples
//
MACS2_CONSENSUS (
ch_antibody_peaks,
is_narrow_peak
)
ch_versions = ch_versions.mix(MACS2_CONSENSUS.out.versions)

//
// 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)

//
// 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)
}

// 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 }

//
// Quantify peaks across samples with featureCounts
//
SUBREAD_FEATURECOUNTS (
ch_bam_saf
)
ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions)

//
// 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)
}

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 ]

featurecounts_txt = SUBREAD_FEATURECOUNTS.out.counts // channel: [ txt ]
featurecounts_summary = SUBREAD_FEATURECOUNTS.out.summary // channel: [ txt ]

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 ]

versions = ch_versions // channel: [ versions.yml ]
}
128 changes: 26 additions & 102 deletions workflows/chipseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
// MODULE: Loaded from modules/local/
//
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'
include { IGV } from '../modules/local/igv'
include { MULTIQC } from '../modules/local/multiqc'
Expand All @@ -17,15 +16,16 @@ include { MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS } from '../modules/local/multiqc_c
//
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
include { paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_chipseq_pipeline'
include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { ALIGN_STAR } from '../subworkflows/local/align_star'
include { BAM_FILTER_BAMTOOLS } from '../subworkflows/local/bam_filter_bamtools'
include { BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC } from '../subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc'
include { BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER } from '../subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf'
include { paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_chipseq_pipeline'
include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { ALIGN_STAR } from '../subworkflows/local/align_star'
include { BAM_FILTER_BAMTOOLS } from '../subworkflows/local/bam_filter_bamtools'
include { BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC } from '../subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc'
include { BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER } from '../subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf'
include { BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 } from '../subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -476,63 +476,6 @@ workflow CHIPSEQ {
ch_deseq2_pca_multiqc = Channel.empty()
ch_deseq2_clustering_multiqc = Channel.empty()
if (!params.skip_consensus_peaks) {
// Create channels: [ meta , [ peaks ] ]
// Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER.out.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 }

//
// MODULE: Generate consensus peaks across samples
//
MACS2_CONSENSUS (
ch_antibody_peaks,
params.narrow_peak
)
ch_macs2_consensus_bed_lib = MACS2_CONSENSUS.out.bed
ch_macs2_consensus_txt_lib = MACS2_CONSENSUS.out.txt
ch_versions = ch_versions.mix(MACS2_CONSENSUS.out.versions)

if (!params.skip_peak_annotation) {
//
// MODULE: Annotate consensus peaks
//
HOMER_ANNOTATEPEAKS_CONSENSUS (
MACS2_CONSENSUS.out.bed,
ch_fasta,
ch_gtf
)
ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS_CONSENSUS.out.versions)

//
// MODULE: Add boolean fields to annotated consensus peaks to aid filtering
//
ANNOTATE_BOOLEAN_PEAKS (
MACS2_CONSENSUS.out.boolean_txt.join(HOMER_ANNOTATEPEAKS_CONSENSUS.out.txt, by: [0]),
)
ch_versions = ch_versions.mix(ANNOTATE_BOOLEAN_PEAKS.out.versions)
}

// Create channels: [ antibody, [ ip_bams ] ]
ch_ip_control_bam
.map {
Expand All @@ -542,42 +485,23 @@ workflow CHIPSEQ {
.groupTuple()
.set { ch_antibody_bams }

// Create channels: [ meta, [ ip_bams ], saf ]
MACS2_CONSENSUS
.out
.saf
.map {
meta, saf ->
[ meta.id, meta, saf ]
}
.join(ch_antibody_bams)
.map {
antibody, meta, saf, bams ->
[ meta, bams.flatten().sort(), saf ]
}
.set { ch_saf_bams }

//
// MODULE: Quantify peaks across samples with featureCounts
//
SUBREAD_FEATURECOUNTS (
ch_saf_bams
BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 (
BAM_PEAKS_CALL_QC_ANNOTATE_MACS2_HOMER.out.peaks,
ch_antibody_bams,
ch_fasta,
ch_gtf,
ch_deseq2_pca_header,
ch_deseq2_clustering_header,
params.narrow_peak,
params.skip_peak_annotation,
params.skip_deseq2_qc
)
ch_subreadfeaturecounts_multiqc = SUBREAD_FEATURECOUNTS.out.summary
ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first())

if (!params.skip_deseq2_qc) {
//
// MODULE: Generate QC plots with DESeq2
//
DESEQ2_QC (
SUBREAD_FEATURECOUNTS.out.counts,
ch_deseq2_pca_header,
ch_deseq2_clustering_header
)
ch_deseq2_pca_multiqc = DESEQ2_QC.out.pca_multiqc
ch_deseq2_clustering_multiqc = DESEQ2_QC.out.dists_multiqc
}
ch_macs2_consensus_bed_lib = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.consensus_bed
ch_macs2_consensus_txt_lib = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.consensus_txt
ch_subreadfeaturecounts_multiqc = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.featurecounts_summary
ch_deseq2_pca_multiqc = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_pca_multiqc
ch_deseq2_clustering_multiqc = BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.deseq2_qc_dists_multiqc
ch_versions = ch_versions.mix(BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2.out.versions)
}

//
Expand Down
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