From d13047f06363cbca1829dccae7a5b550f0144c03 Mon Sep 17 00:00:00 2001 From: Venkat Malladi <venkat.malladi@utsouthwestern.edu> Date: Sun, 21 Apr 2019 12:01:44 -0500 Subject: [PATCH] Revert changes. --- workflow/main.nf | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/workflow/main.nf b/workflow/main.nf index 0ec6e17..3045aaa 100644 --- a/workflow/main.nf +++ b/workflow/main.nf @@ -168,7 +168,7 @@ process alignReads { output: 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 script: @@ -207,9 +207,9 @@ process filterReads { 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 - file('*.flagstat.qc') into dedupReadsStats - file('*.pbc.qc') into dedupReadsComplexity - file('*.dedup.qc') into dupReads + file '*.flagstat.qc' into dedupReadsStats + file '*.pbc.qc' into dedupReadsComplexity + file '*.dedup.qc' into dupReads file('version_*.txt') into filterReadsVersions script: @@ -254,7 +254,7 @@ process experimentQC { output: - file('*.{pdf,npz}') into experimentQCStats + file '*.{pdf,npz}' into experimentQCStats file('version_*.txt') into experimentQCVersions script: @@ -354,7 +354,7 @@ process defineExpDesignFiles { output: - file('*.tsv') into experimentObjs mode flatten + file '*.tsv' into experimentObjs mode flatten script: @@ -379,7 +379,7 @@ process poolAndPsuedoReads { output: - file('*.tsv') into experimentPoolObjs + file '*.tsv' into experimentPoolObjs script: @@ -415,7 +415,7 @@ process callPeaksMACS { output: 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 script: @@ -462,11 +462,11 @@ process consensusPeaks { output: - file('*.replicated.*') into consensusPeaks - file('*.rejected.*') into rejectedPeaks - file('design_diffPeaks.csv') into designDiffPeaks - file('design_annotatePeaks.tsv') into designAnnotatePeaks, designMotifSearch - file('unique_experiments.csv') into uniqueExperiments + file '*.replicated.*' into consensusPeaks + file '*.rejected.*' into rejectedPeaks + file 'design_diffPeaks.csv' into designDiffPeaks + file 'design_annotatePeaks.tsv' into designAnnotatePeaks, designMotifSearch + file 'unique_experiments.csv' into uniqueExperiments file('version_*.txt') into consensusPeaksVersions script: @@ -490,7 +490,7 @@ process peakAnnotation { output: - file("*chipseeker*") into peakAnnotation + file "*chipseeker*" into peakAnnotation file('version_*.txt') into peakAnnotationVersions script: @@ -513,8 +513,8 @@ process motifSearch { output: - file("*memechip") into motifSearch - file("*narrowPeak") into filteredPeaks + file "*memechip" into motifSearch + file "*narrowPeak" into filteredPeaks file('version_*.txt') into motifSearchVersions when: @@ -545,10 +545,10 @@ process diffPeaks { output: - file('*_diffbind.bed') into diffPeaks - file('*_diffbind.csv') into diffPeaksCounts - file('*.pdf') into diffPeaksStats - file('normcount_peaksets.txt') into normCountPeaks + file '*_diffbind.bed' into diffPeaks + file '*_diffbind.csv' into diffPeaksCounts + file '*.pdf' into diffPeaksStats + file 'normcount_peaksets.txt' into normCountPeaks file('version_*.txt') into diffPeaksVersions when: @@ -592,8 +592,8 @@ process multiqcReport { file('software_versions_mqc.yaml') into softwareVersions file('software_references_mqc.yaml') into softwareReferences - file('multiqc_report.html') into multiqcReport - file("*_data") into multiqcData + file "multiqc_report.html" into multiqcReport + file "*_data" in multiqcData script: -- GitLab