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:
--
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