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Commit 6ae5df58 authored by Venkat Malladi's avatar Venkat Malladi
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Fix syntax.

parent 8e0a5bd9
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1 merge request!23Resolve "Output software versions and methods and references"
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...@@ -134,7 +134,7 @@ process alignReads { ...@@ -134,7 +134,7 @@ 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:
...@@ -166,9 +166,9 @@ process filterReads { ...@@ -166,9 +166,9 @@ 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:
...@@ -204,7 +204,7 @@ process experimentQC { ...@@ -204,7 +204,7 @@ 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:
...@@ -293,7 +293,7 @@ process defineExpDesignFiles { ...@@ -293,7 +293,7 @@ process defineExpDesignFiles {
output: output:
file '*.tsv' into experimentObjs mode flatten file('*.tsv') into experimentObjs mode flatten
script: script:
...@@ -317,7 +317,7 @@ process poolAndPsuedoReads { ...@@ -317,7 +317,7 @@ process poolAndPsuedoReads {
output: output:
file '*.tsv' into experimentPoolObjs file('*.tsv') into experimentPoolObjs
script: script:
...@@ -351,7 +351,7 @@ process callPeaksMACS { ...@@ -351,7 +351,7 @@ 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:
...@@ -388,11 +388,11 @@ process consensusPeaks { ...@@ -388,11 +388,11 @@ 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:
...@@ -414,7 +414,7 @@ process peakAnnotation { ...@@ -414,7 +414,7 @@ process peakAnnotation {
output: output:
file "*chipseeker*" into peakAnnotation file("*chipseeker*") into peakAnnotation
file('version_*.txt') into peakAnnotationVersions file('version_*.txt') into peakAnnotationVersions
script: script:
...@@ -436,8 +436,8 @@ process motifSearch { ...@@ -436,8 +436,8 @@ 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
script: script:
...@@ -463,10 +463,10 @@ process diffPeaks { ...@@ -463,10 +463,10 @@ 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:
...@@ -494,10 +494,12 @@ process softwareReport { ...@@ -494,10 +494,12 @@ process softwareReport {
motifSearchVersions motifSearchVersions
diffPeaksVersions diffPeaksVersions
experimentQCVersions experimentQCVersions
references
output: output:
file '*_mqc.yaml' into softwareVersions file('*_mqc.yaml') into softwareVersions
file '*_mqc.yaml' into softwareReferences file('*_mqc.txt') into softwareReferences
script: script:
""" """
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