From 6b279430c1a73da2ef77fd0b33cf2dc2123aa4f3 Mon Sep 17 00:00:00 2001 From: Venkat Malladi <venkat.malladi@utsouthwestern.edu> Date: Sun, 21 Apr 2019 11:41:02 -0500 Subject: [PATCH] Consistent with output syntax. --- workflow/main.nf | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/workflow/main.nf b/workflow/main.nf index 3045aaa..0ec6e17 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" in multiqcData + file('multiqc_report.html') into multiqcReport + file("*_data") into multiqcData script: -- GitLab