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JoseEspinosaJoseEspinosa
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Update all code using macs2 to use macs3, also docs
1 parent dabbe8c commit 01623d6

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+127
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lines changed

‎CITATIONS.md

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@@ -46,7 +46,7 @@
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> Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89. doi: 10.1016/j.molcel.2010.05.004. PubMed PMID: 20513432; PubMed Central PMCID: PMC2898526.
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- [MACS2](https://www.ncbi.nlm.nih.gov/pubmed/18798982/)
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- [MACS3](https://www.ncbi.nlm.nih.gov/pubmed/18798982/)
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> Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715.
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‎README.md

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@@ -59,7 +59,7 @@ You can find numerous talks on the [nf-core events page](https://nf-co.re/events
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5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))
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6. Calculate genome-wide IP enrichment relative to control ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
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7. Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC ([`phantompeakqualtools`](https://github.com/kundajelab/phantompeakqualtools))
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8. Call broad/narrow peaks ([`MACS2`](https://github.com/macs3-project/MACS))
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8. Call broad/narrow peaks ([`MACS3`](https://github.com/macs3-project/MACS))
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9. Annotate peaks relative to gene features ([`HOMER`](http://homer.ucsd.edu/homer/download.html))
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10. Create consensus peakset across all samples and create tabular file to aid in the filtering of the data ([`BEDTools`](https://github.com/arq5x/bedtools2/))
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11. Count reads in consensus peaks ([`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))

‎assets/multiqc/frip_score_header.txt

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Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
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#id: 'frip_score'
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#section_name: 'MERGED LIB: MACS2 FRiP score'
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#section_name: 'MERGED LIB: MACS3 FRiP score'
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#description: "is generated by calculating the fraction of all mapped reads that fall
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# into the MACS2 called peak regions. A read must overlap a peak by at least 20% to be counted.
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# into the MACS3 called peak regions. A read must overlap a peak by at least 20% to be counted.
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# See <a href='https://www.encodeproject.org/data-standards/terms/' target='_blank'>FRiP score</a>."
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#plot_type: 'bargraph'
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#anchor: 'frip_score'

‎assets/multiqc/peak_count_header.txt

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@@ -1,7 +1,7 @@
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#id: 'peak_count'
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#section_name: 'MERGED LIB: MACS2 peak count'
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#section_name: 'MERGED LIB: MACS3 peak count'
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#description: "is calculated from total number of peaks called by
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# <a href='https://github.com/taoliu/MACS' target='_blank'>MACS2</a>"
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# <a href='https://github.com/taoliu/MACS' target='_blank'>MACS3</a>"
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#plot_type: 'bargraph'
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#anchor: 'peak_count'
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#pconfig:

‎assets/multiqc_config.yml

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@@ -72,7 +72,7 @@ module_order:
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anchor: "mlib_featurecounts"
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info: "This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks."
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path_filters:
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- "./macs2/featurecounts/*.summary"
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- "./macs3/featurecounts/*.summary"
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report_section_order:
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peak_count:

‎assets/schema_input.json

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@@ -33,15 +33,30 @@
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}
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]
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},
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"replicate": {
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"type": "integer",
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"errorMessage": "Replicate id not an integer!",
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"meta": ["replicate"]
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},
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"antibody": {
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"type": "string",
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"pattern": "^\\S+$",
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"errorMessage": "Antibody entry cannot contain spaces"
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"errorMessage": "Antibody entry cannot contain spaces",
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"dependentRequired": ["control"],
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"meta": ["antibody"]
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},
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"control": {
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"type": "string",
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"pattern": "^\\S+$",
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"errorMessage": "Control entry cannot contain spaces"
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"errorMessage": "Control entry cannot contain spaces",
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"dependentRequired": ["antibody", "control_replicate"],
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"meta": ["control"]
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},
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"control_replicate": {
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"type": "string",
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"pattern": "^\\S+$",
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"errorMessage": "Control entry cannot contain spaces",
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"meta": ["control_replicate"]
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}
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},
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"required": ["sample", "fastq_1"]

‎bin/macs2_merged_expand.py ‎bin/macs3_merged_expand.py

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@@ -17,15 +17,15 @@
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############################################
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Description = "Add sample boolean files and aggregate columns from merged MACS narrow or broad peak file."
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Epilog = """Example usage: python macs2_merged_expand.py <MERGED_INTERVAL_FILE> <SAMPLE_NAME_LIST> <OUTFILE> --is_narrow_peak --min_replicates 1"""
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Epilog = """Example usage: python macs3_merged_expand.py <MERGED_INTERVAL_FILE> <SAMPLE_NAME_LIST> <OUTFILE> --is_narrow_peak --min_replicates 1"""
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argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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2424
## REQUIRED PARAMETERS
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argParser.add_argument("MERGED_INTERVAL_FILE", help="Merged MACS2 interval file created using linux sort and mergeBed.")
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argParser.add_argument("MERGED_INTERVAL_FILE", help="Merged MACS3 interval file created using linux sort and mergeBed.")
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argParser.add_argument(
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"SAMPLE_NAME_LIST",
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help="Comma-separated list of sample names as named in individual MACS2 broadPeak/narrowPeak output file e.g. SAMPLE_R1 for SAMPLE_R1_peak_1.",
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help="Comma-separated list of sample names as named in individual MACS3 broadPeak/narrowPeak output file e.g. SAMPLE_R1 for SAMPLE_R1_peak_1.",
2929
)
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argParser.add_argument("OUTFILE", help="Full path to output directory.")
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@@ -76,7 +76,7 @@ def makedir(path):
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## sort -k1,1 -k2,2n <MACS_NARROWPEAK_FILE_LIST> | mergeBed -c 2,3,4,5,6,7,8,9,10 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > merged_peaks.txt
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7878

79-
def macs2_merged_expand(MergedIntervalTxtFile, SampleNameList, OutFile, isNarrow=False, minReplicates=1):
79+
def macs3_merged_expand(MergedIntervalTxtFile, SampleNameList, OutFile, isNarrow=False, minReplicates=1):
8080
makedir(os.path.dirname(OutFile))
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8282
combFreqDict = {}
@@ -208,7 +208,7 @@ def macs2_merged_expand(MergedIntervalTxtFile, SampleNameList, OutFile, isNarrow
208208
############################################
209209
############################################
210210

211-
macs2_merged_expand(
211+
macs3_merged_expand(
212212
MergedIntervalTxtFile=args.MERGED_INTERVAL_FILE,
213213
SampleNameList=args.SAMPLE_NAME_LIST.split(","),
214214
OutFile=args.OUTFILE,

‎bin/plot_macs2_qc.r ‎bin/plot_macs3_qc.r

+1-1
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@@ -20,7 +20,7 @@ library(scales)
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option_list <- list(make_option(c("-i", "--peak_files"), type="character", default=NULL, help="Comma-separated list of peak files.", metavar="path"),
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make_option(c("-s", "--sample_ids"), type="character", default=NULL, help="Comma-separated list of sample ids associated with peak files. Must be unique and in same order as peaks files input.", metavar="string"),
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make_option(c("-o", "--outdir"), type="character", default='./', help="Output directory", metavar="path"),
23-
make_option(c("-p", "--outprefix"), type="character", default='macs2_peakqc', help="Output prefix", metavar="string"))
23+
make_option(c("-p", "--outprefix"), type="character", default='macs3_peakqc', help="Output prefix", metavar="string"))
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2525
opt_parser <- OptionParser(option_list=option_list)
2626
opt <- parse_args(opt_parser)

‎conf/modules.config

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@@ -540,7 +540,7 @@ if (!params.skip_plot_fingerprint) {
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}
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542542
process {
543-
withName: 'MACS2_CALLPEAK' {
543+
withName: 'MACS3_CALLPEAK' {
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ext.args = [
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'--keep-dup all',
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params.narrow_peak ? '' : "--broad --broad-cutoff ${params.broad_cutoff}",
@@ -551,7 +551,7 @@ process {
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].join(' ').trim()
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publishDir = [
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path: { [
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"${params.outdir}/${params.aligner}/merged_library/macs2",
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"${params.outdir}/${params.aligner}/merged_library/macs3",
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params.narrow_peak? '/narrow_peak' : '/broad_peak'
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].join('') },
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mode: params.publish_dir_mode,
@@ -562,14 +562,14 @@ process {
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withName: 'FRIP_SCORE' {
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ext.args = '-bed -c -f 0.20'
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publishDir = [
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path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
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path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
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enabled: false
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]
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}
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withName: 'MULTIQC_CUSTOM_PEAKS' {
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publishDir = [
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path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
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path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
@@ -578,11 +578,11 @@ process {
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579579
if (!params.skip_peak_annotation) {
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process {
581-
withName: 'HOMER_ANNOTATEPEAKS_MACS2' {
581+
withName: 'HOMER_ANNOTATEPEAKS_MACS3' {
582582
ext.args = '-gid'
583583
ext.prefix = { "${meta.id}_peaks" }
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publishDir = [
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path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
585+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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592592
if (!params.skip_peak_qc) {
593593
process {
594-
withName: 'PLOT_MACS2_QC' {
595-
ext.args = '-o ./ -p macs2_peak'
594+
withName: 'PLOT_MACS3_QC' {
595+
ext.args = '-o ./ -p macs3_peak'
596596
publishDir = [
597-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
597+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
601601
}
602602

603603
withName: 'PLOT_HOMER_ANNOTATEPEAKS' {
604604
ext.args = '-o ./'
605-
ext.prefix = 'macs2_annotatePeaks'
605+
ext.prefix = 'macs3_annotatePeaks'
606606
publishDir = [
607-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
607+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
608608
mode: params.publish_dir_mode,
609609
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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615615

616616
if (!params.skip_consensus_peaks) {
617617
process {
618-
withName: 'MACS2_CONSENSUS' {
618+
withName: 'MACS3_CONSENSUS' {
619619
ext.when = { meta.multiple_groups || meta.replicates_exist }
620620
ext.prefix = { "${meta.id}.consensus_peaks" }
621621
publishDir = [
622-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
622+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
@@ -629,7 +629,7 @@ if (!params.skip_consensus_peaks) {
629629
ext.args = '-F SAF -O --fracOverlap 0.2'
630630
ext.prefix = { "${meta.id}.consensus_peaks" }
631631
publishDir = [
632-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
632+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
633633
mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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642642
ext.args = '-gid'
643643
ext.prefix = { "${meta.id}.consensus_peaks" }
644644
publishDir = [
645-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
645+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
646646
mode: params.publish_dir_mode,
647647
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
648648
]
@@ -651,7 +651,7 @@ if (!params.skip_consensus_peaks) {
651651
withName: 'ANNOTATE_BOOLEAN_PEAKS' {
652652
ext.prefix = { "${meta.id}.consensus_peaks" }
653653
publishDir = [
654-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
654+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}" },
655655
mode: params.publish_dir_mode,
656656
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
657657
]
@@ -671,7 +671,7 @@ if (!params.skip_consensus_peaks) {
671671
].join(' ').trim()
672672
ext.prefix = { "${meta.id}.consensus_peaks" }
673673
publishDir = [
674-
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}/deseq2" },
674+
path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/${meta.id}/deseq2" },
675675
mode: params.publish_dir_mode,
676676
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]

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