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Commit d13047f0 authored by Venkat Malladi's avatar Venkat Malladi
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Revert changes.

parent 927e1f94
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1 merge request!26Resolve "Add multiqc summary of data"
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...@@ -168,7 +168,7 @@ process alignReads { ...@@ -168,7 +168,7 @@ process alignReads {
output: output:
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into mappedReads set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into mappedReads
file('*.flagstat.qc') into mappedReadsStats file '*.flagstat.qc' into mappedReadsStats
file('version_*.txt') into alignReadsVersions file('version_*.txt') into alignReadsVersions
script: script:
...@@ -207,9 +207,9 @@ process filterReads { ...@@ -207,9 +207,9 @@ process filterReads {
set sampleId, file('*.bam'), file('*.bai'), experimentId, biosample, factor, treatment, replicate, controlId into dedupReads set sampleId, file('*.bam'), file('*.bai'), experimentId, biosample, factor, treatment, replicate, controlId into dedupReads
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into convertReads set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into convertReads
file('*.flagstat.qc') into dedupReadsStats file '*.flagstat.qc' into dedupReadsStats
file('*.pbc.qc') into dedupReadsComplexity file '*.pbc.qc' into dedupReadsComplexity
file('*.dedup.qc') into dupReads file '*.dedup.qc' into dupReads
file('version_*.txt') into filterReadsVersions file('version_*.txt') into filterReadsVersions
script: script:
...@@ -254,7 +254,7 @@ process experimentQC { ...@@ -254,7 +254,7 @@ process experimentQC {
output: output:
file('*.{pdf,npz}') into experimentQCStats file '*.{pdf,npz}' into experimentQCStats
file('version_*.txt') into experimentQCVersions file('version_*.txt') into experimentQCVersions
script: script:
...@@ -354,7 +354,7 @@ process defineExpDesignFiles { ...@@ -354,7 +354,7 @@ process defineExpDesignFiles {
output: output:
file('*.tsv') into experimentObjs mode flatten file '*.tsv' into experimentObjs mode flatten
script: script:
...@@ -379,7 +379,7 @@ process poolAndPsuedoReads { ...@@ -379,7 +379,7 @@ process poolAndPsuedoReads {
output: output:
file('*.tsv') into experimentPoolObjs file '*.tsv' into experimentPoolObjs
script: script:
...@@ -415,7 +415,7 @@ process callPeaksMACS { ...@@ -415,7 +415,7 @@ process callPeaksMACS {
output: output:
set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks set sampleId, file('*.narrowPeak'), file('*.fc_signal.bw'), file('*.pvalue_signal.bw'), experimentId, biosample, factor, treatment, replicate, controlId into experimentPeaks
file('*.xls') into callPeaksMACSsummit file '*.xls' into callPeaksMACSsummit
file('version_*.txt') into callPeaksMACSVersions file('version_*.txt') into callPeaksMACSVersions
script: script:
...@@ -462,11 +462,11 @@ process consensusPeaks { ...@@ -462,11 +462,11 @@ process consensusPeaks {
output: output:
file('*.replicated.*') into consensusPeaks file '*.replicated.*' into consensusPeaks
file('*.rejected.*') into rejectedPeaks file '*.rejected.*' into rejectedPeaks
file('design_diffPeaks.csv') into designDiffPeaks file 'design_diffPeaks.csv' into designDiffPeaks
file('design_annotatePeaks.tsv') into designAnnotatePeaks, designMotifSearch file 'design_annotatePeaks.tsv' into designAnnotatePeaks, designMotifSearch
file('unique_experiments.csv') into uniqueExperiments file 'unique_experiments.csv' into uniqueExperiments
file('version_*.txt') into consensusPeaksVersions file('version_*.txt') into consensusPeaksVersions
script: script:
...@@ -490,7 +490,7 @@ process peakAnnotation { ...@@ -490,7 +490,7 @@ process peakAnnotation {
output: output:
file("*chipseeker*") into peakAnnotation file "*chipseeker*" into peakAnnotation
file('version_*.txt') into peakAnnotationVersions file('version_*.txt') into peakAnnotationVersions
script: script:
...@@ -513,8 +513,8 @@ process motifSearch { ...@@ -513,8 +513,8 @@ process motifSearch {
output: output:
file("*memechip") into motifSearch file "*memechip" into motifSearch
file("*narrowPeak") into filteredPeaks file "*narrowPeak" into filteredPeaks
file('version_*.txt') into motifSearchVersions file('version_*.txt') into motifSearchVersions
when: when:
...@@ -545,10 +545,10 @@ process diffPeaks { ...@@ -545,10 +545,10 @@ process diffPeaks {
output: output:
file('*_diffbind.bed') into diffPeaks file '*_diffbind.bed' into diffPeaks
file('*_diffbind.csv') into diffPeaksCounts file '*_diffbind.csv' into diffPeaksCounts
file('*.pdf') into diffPeaksStats file '*.pdf' into diffPeaksStats
file('normcount_peaksets.txt') into normCountPeaks file 'normcount_peaksets.txt' into normCountPeaks
file('version_*.txt') into diffPeaksVersions file('version_*.txt') into diffPeaksVersions
when: when:
...@@ -592,8 +592,8 @@ process multiqcReport { ...@@ -592,8 +592,8 @@ process multiqcReport {
file('software_versions_mqc.yaml') into softwareVersions file('software_versions_mqc.yaml') into softwareVersions
file('software_references_mqc.yaml') into softwareReferences file('software_references_mqc.yaml') into softwareReferences
file('multiqc_report.html') into multiqcReport file "multiqc_report.html" into multiqcReport
file("*_data") into multiqcData file "*_data" in multiqcData
script: script:
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