From 6ae5df587ce63227d1b3e548588b4ecbe1c5ddb3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 12 Mar 2019 08:38:46 -0500
Subject: [PATCH] Fix syntax.
---
workflow/main.nf | 46 ++++++++++++++++++++++++----------------------
1 file changed, 24 insertions(+), 22 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 55fd065..420a0c7 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -134,7 +134,7 @@ 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:
@@ -166,9 +166,9 @@ 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:
@@ -204,7 +204,7 @@ process experimentQC {
output:
- file '*.{pdf,npz}' into experimentQCStats
+ file('*.{pdf,npz}') into experimentQCStats
file('version_*.txt') into experimentQCVersions
script:
@@ -293,7 +293,7 @@ process defineExpDesignFiles {
output:
- file '*.tsv' into experimentObjs mode flatten
+ file('*.tsv') into experimentObjs mode flatten
script:
@@ -317,7 +317,7 @@ process poolAndPsuedoReads {
output:
- file '*.tsv' into experimentPoolObjs
+ file('*.tsv') into experimentPoolObjs
script:
@@ -351,7 +351,7 @@ 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:
@@ -388,11 +388,11 @@ 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:
@@ -414,7 +414,7 @@ process peakAnnotation {
output:
- file "*chipseeker*" into peakAnnotation
+ file("*chipseeker*") into peakAnnotation
file('version_*.txt') into peakAnnotationVersions
script:
@@ -436,8 +436,8 @@ process motifSearch {
output:
- file "*memechip" into motifSearch
- file "*narrowPeak" into filteredPeaks
+ file("*memechip") into motifSearch
+ file("*narrowPeak") into filteredPeaks
file('version_*.txt') into motifSearchVersions
script:
@@ -463,10 +463,10 @@ 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:
@@ -494,10 +494,12 @@ process softwareReport {
motifSearchVersions
diffPeaksVersions
experimentQCVersions
+ references
+
output:
- file '*_mqc.yaml' into softwareVersions
- file '*_mqc.yaml' into softwareReferences
+ file('*_mqc.yaml') into softwareVersions
+ file('*_mqc.txt') into softwareReferences
script:
"""
--
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