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Merge pull request #228 from nf-core/computemarix-tssfix-193
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Computemarix tssfix 193
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@drpatelh
drpatelh authored Nov 22, 2022
2 parents f012a49 + aea3caf commit 54e8e52
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Showing 2 changed files with 41 additions and 20 deletions.
14 changes: 12 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -483,8 +483,8 @@ if (!params.skip_preseq) {

if (!params.skip_plot_profile) {
process {
withName: 'DEEPTOOLS_COMPUTEMATRIX' {
ext.args = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --skipZeros --smartLabels'
withName: 'DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS' {
ext.args = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
ext.prefix = { "${meta.id}.mLb.clN" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/deeptools/plotprofile" },
Expand All @@ -493,6 +493,16 @@ if (!params.skip_plot_profile) {
]
}

withName: 'DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT' {
ext.args = 'reference-point --missingDataAsZero --skipZeros --smartLabels --upstream 3000 --downstream 3000'
ext.prefix = { "${meta.id}.mLb.clN.point" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/deeptools/plotprofile" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'DEEPTOOLS_PLOTPROFILE' {
ext.prefix = { "${meta.id}.mLb.clN" }
publishDir = [
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47 changes: 29 additions & 18 deletions workflows/atacseq.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,6 @@ include { FILTER_BAM_BAMTOOLS } from '../subworkflows/local/filter_bam_bamtools'

include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics/main'
include { PRESEQ_LCEXTRAP } from '../modules/nf-core/preseq/lcextrap/main'
include { DEEPTOOLS_COMPUTEMATRIX } from '../modules/nf-core/deeptools/computematrix/main'
include { DEEPTOOLS_PLOTPROFILE } from '../modules/nf-core/deeptools/plotprofile/main'
include { DEEPTOOLS_PLOTHEATMAP } from '../modules/nf-core/deeptools/plotheatmap/main'
include { DEEPTOOLS_PLOTFINGERPRINT } from '../modules/nf-core/deeptools/plotfingerprint/main'
Expand All @@ -108,18 +107,21 @@ include { ATAQV_ATAQV } from '../modules/nf-core/ataqv/ataqv/m
include { ATAQV_MKARV } from '../modules/nf-core/ataqv/mkarv/main'
include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'

include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_LIBRARY } from '../modules/nf-core/picard/mergesamfiles/main'
include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_REPLICATE } from '../modules/nf-core/picard/mergesamfiles/main'
include { UCSC_BEDGRAPHTOBIGWIG as UCSC_BEDGRAPHTOBIGWIG_LIBRARY } from '../modules/nf-core/ucsc/bedgraphtobigwig/main'
include { UCSC_BEDGRAPHTOBIGWIG as UCSC_BEDGRAPHTOBIGWIG_REPLICATE } from '../modules/nf-core/ucsc/bedgraphtobigwig/main'
include { MACS2_CALLPEAK as MACS2_CALLPEAK_LIBRARY } from '../modules/nf-core/macs2/callpeak/main'
include { MACS2_CALLPEAK as MACS2_CALLPEAK_REPLICATE } from '../modules/nf-core/macs2/callpeak/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_MACS2_LIBRARY } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_MACS2_REPLICATE } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_CONSENSUS_LIBRARY } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_CONSENSUS_REPLICATE } from '../modules/nf-core/homer/annotatepeaks/main'
include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_LIBRARY } from '../modules/nf-core/subread/featurecounts/main'
include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_REPLICATE } from '../modules/nf-core/subread/featurecounts/main'

include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS } from '../modules/nf-core/deeptools/computematrix/main'
include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT } from '../modules/nf-core/deeptools/computematrix/main'
include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_LIBRARY } from '../modules/nf-core/picard/mergesamfiles/main'
include { PICARD_MERGESAMFILES as PICARD_MERGESAMFILES_REPLICATE } from '../modules/nf-core/picard/mergesamfiles/main'
include { UCSC_BEDGRAPHTOBIGWIG as UCSC_BEDGRAPHTOBIGWIG_LIBRARY } from '../modules/nf-core/ucsc/bedgraphtobigwig/main'
include { UCSC_BEDGRAPHTOBIGWIG as UCSC_BEDGRAPHTOBIGWIG_REPLICATE } from '../modules/nf-core/ucsc/bedgraphtobigwig/main'
include { MACS2_CALLPEAK as MACS2_CALLPEAK_LIBRARY } from '../modules/nf-core/macs2/callpeak/main'
include { MACS2_CALLPEAK as MACS2_CALLPEAK_REPLICATE } from '../modules/nf-core/macs2/callpeak/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_MACS2_LIBRARY } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_MACS2_REPLICATE } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_CONSENSUS_LIBRARY } from '../modules/nf-core/homer/annotatepeaks/main'
include { HOMER_ANNOTATEPEAKS as HOMER_ANNOTATEPEAKS_CONSENSUS_REPLICATE } from '../modules/nf-core/homer/annotatepeaks/main'
include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_LIBRARY } from '../modules/nf-core/subread/featurecounts/main'
include { SUBREAD_FEATURECOUNTS as SUBREAD_FEATURECOUNTS_REPLICATE } from '../modules/nf-core/subread/featurecounts/main'

//
// SUBWORKFLOW: Consisting entirely of nf-core/modules
Expand Down Expand Up @@ -366,19 +368,28 @@ workflow ATACSEQ {
ch_deeptoolsplotprofile_multiqc = Channel.empty()
if (!params.skip_plot_profile) {
//
// MODULE: deepTools matrix generation for plotting
// MODULE: deepTools matrix generation for plotting over full transcript length
//
DEEPTOOLS_COMPUTEMATRIX (
DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS (
UCSC_BEDGRAPHTOBIGWIG_LIBRARY.out.bigwig,
PREPARE_GENOME.out.gene_bed
)
ch_versions = ch_versions.mix(DEEPTOOLS_COMPUTEMATRIX.out.versions.first())
ch_versions = ch_versions.mix(DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS.out.versions.first())

//
// MODULE: deepTools matrix generation for plotting at TSS point
//
DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT (
UCSC_BEDGRAPHTOBIGWIG_LIBRARY.out.bigwig,
PREPARE_GENOME.out.tss_bed
)
ch_versions = ch_versions.mix(DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT.out.versions.first())

//
// MODULE: deepTools profile plots
//
DEEPTOOLS_PLOTPROFILE (
DEEPTOOLS_COMPUTEMATRIX.out.matrix
DEEPTOOLS_COMPUTEMATRIX_SCALE_REGIONS.out.matrix
)
ch_deeptoolsplotprofile_multiqc = DEEPTOOLS_PLOTPROFILE.out.table
ch_versions = ch_versions.mix(DEEPTOOLS_PLOTPROFILE.out.versions.first())
Expand All @@ -387,7 +398,7 @@ workflow ATACSEQ {
// MODULE: deepTools heatmaps
//
DEEPTOOLS_PLOTHEATMAP (
DEEPTOOLS_COMPUTEMATRIX.out.matrix
DEEPTOOLS_COMPUTEMATRIX_REFERENCE_POINT.out.matrix
)
ch_versions = ch_versions.mix(DEEPTOOLS_PLOTHEATMAP.out.versions.first())
}
Expand Down

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