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Merge pull request #355 from bjlang/dev
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Fix double slash in directory urls
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@JoseEspinosa
JoseEspinosa committed Mar 20, 2024
2 parents a4b97cb + 3687239 commit fdc35e7
Showing 1 changed file with 24 additions and 24 deletions.
48 changes: 24 additions & 24 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -601,7 +601,7 @@ process {
].join(' ').trim()
ext.prefix = { "${meta.id}.mLb.clN" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -610,15 +610,15 @@ process {
withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:FRIP_SCORE' {
ext.args = '-bed -c -f 0.20'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
enabled: false
]
}

withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:MULTIQC_CUSTOM_PEAKS' {
ext.prefix = { "${meta.id}.mLb.clN_peaks" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -631,7 +631,7 @@ if (!params.skip_peak_annotation) {
ext.args = '-gid'
ext.prefix = { "${meta.id}.mLb.clN_peaks" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -643,7 +643,7 @@ if (!params.skip_peak_annotation) {
withName: '.*:MERGED_LIBRARY_CALL_ANNOTATE_PEAKS:PLOT_MACS2_QC' {
ext.args = '-o ./ -p macs2_peak.mLb.clN'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -653,7 +653,7 @@ if (!params.skip_peak_annotation) {
ext.args = '-o ./'
ext.prefix = 'macs2_annotatePeaks.mLb.clN'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -668,7 +668,7 @@ if (!params.skip_consensus_peaks) {
ext.args = "--min_replicates ${params.min_reps_consensus}"
ext.prefix = "consensus_peaks.mLb.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -678,7 +678,7 @@ if (!params.skip_consensus_peaks) {
ext.args = '-F SAF -O --fracOverlap 0.2'
ext.prefix = "consensus_peaks.mLb.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -696,7 +696,7 @@ if (!params.skip_consensus_peaks) {
].join(' ').trim()
ext.prefix = { "${meta.id}.mLb.clN" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/deseq2" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/deseq2" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -711,7 +711,7 @@ if (!params.skip_peak_annotation) {
ext.args = '-gid'
ext.prefix = "consensus_peaks.mLb.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -724,14 +724,14 @@ if (!params.skip_ataqv) {
withName: 'MERGED_LIBRARY_ATAQV_ATAQV' {
ext.args = '--ignore-read-groups'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/ataqv/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_library/ataqv/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'MERGED_LIBRARY_ATAQV_MKARV' {
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_library/ataqv/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_library/ataqv/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand Down Expand Up @@ -825,7 +825,7 @@ if (!params.skip_merge_replicates) {
].join(' ').trim()
ext.prefix = { "${meta.id}.mRp.clN" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -834,15 +834,15 @@ if (!params.skip_merge_replicates) {
withName: '.*:MERGED_REPLICATE_CALL_ANNOTATE_PEAKS:FRIP_SCORE' {
ext.args = '-bed -c -f 0.20'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
enabled: false
]
}

withName: '.*:MERGED_REPLICATE_CALL_ANNOTATE_PEAKS:MULTIQC_CUSTOM_PEAKS' {
ext.prefix = { "${meta.id}.mRp.clN_peaks" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -855,7 +855,7 @@ if (!params.skip_merge_replicates) {
ext.args = '-gid'
ext.prefix = { "${meta.id}.mRp.clN_peaks" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -867,7 +867,7 @@ if (!params.skip_merge_replicates) {
withName: '.*:MERGED_REPLICATE_CALL_ANNOTATE_PEAKS:PLOT_MACS2_QC' {
ext.args = '-o ./ -p macs2_peak.mRp.clN'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -877,7 +877,7 @@ if (!params.skip_merge_replicates) {
ext.args = '-o ./'
ext.prefix = 'macs2_annotatePeaks.mRp.clN'
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -891,7 +891,7 @@ if (!params.skip_merge_replicates) {
withName: '.*:MERGED_REPLICATE_CONSENSUS_PEAKS:MACS2_CONSENSUS' {
ext.prefix = "consensus_peaks.mRp.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -901,7 +901,7 @@ if (!params.skip_merge_replicates) {
ext.args = '-F SAF -O --fracOverlap 0.2'
ext.prefix = "consensus_peaks.mRp.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -919,7 +919,7 @@ if (!params.skip_merge_replicates) {
].join(' ').trim()
ext.prefix = { "${meta.id}.mRp.clN" }
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus/deseq2" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/deseq2" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -934,7 +934,7 @@ if (!params.skip_merge_replicates) {
ext.args = '-gid'
ext.prefix = "consensus_peaks.mRp.clN"
publishDir = [
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/consensus" },
path: { "${params.outdir}/${params.aligner}/merged_replicate/macs2/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand All @@ -948,7 +948,7 @@ if (!params.skip_igv) {
withName: 'IGV' {
publishDir = [
[
path: { "${params.outdir}/igv/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/igv/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
pattern: '*.{txt,xml}'
],
Expand All @@ -967,7 +967,7 @@ if (!params.skip_multiqc) {
withName: 'MULTIQC' {
ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
publishDir = [
path: { "${params.outdir}/multiqc/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}" },
path: { "${params.outdir}/multiqc/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
Expand Down

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