From a7b0a5a8c6faa841833d1ff930ac874dc6e98cdf Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 12 Mar 2019 08:53:39 -0500
Subject: [PATCH] Fix main.
---
workflow/main.nf | 45 +++++++++++++++++++++------------------------
1 file changed, 21 insertions(+), 24 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index a659f8e..b2f7806 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -47,7 +47,6 @@ cutoffRatio = params.cutoffRatio
outDir = params.outDir
extendReadsLen = params.extendReadsLen
topPeakCount = params.topPeakCount
-references = params.references
// Check design file for errors
process checkDesignFile {
@@ -134,7 +133,7 @@ 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 +165,9 @@ 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 +203,7 @@ process experimentQC {
output:
- file('*.{pdf,npz}') into experimentQCStats
+ file '*.{pdf,npz}' into experimentQCStats
file('version_*.txt') into experimentQCVersions
script:
@@ -293,7 +292,7 @@ process defineExpDesignFiles {
output:
- file('*.tsv') into experimentObjs mode flatten
+ file '*.tsv' into experimentObjs mode flatten
script:
@@ -317,7 +316,7 @@ process poolAndPsuedoReads {
output:
- file('*.tsv') into experimentPoolObjs
+ file '*.tsv' into experimentPoolObjs
script:
@@ -351,7 +350,7 @@ 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 +387,11 @@ process consensusPeaks {
output:
- file('*.replicated.*') into replicatedPeaks
- 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 +413,7 @@ process peakAnnotation {
output:
- file("*chipseeker*") into peakAnnotation
+ file "*chipseeker*" into peakAnnotation
file('version_*.txt') into peakAnnotationVersions
script:
@@ -436,8 +435,8 @@ 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 +462,10 @@ 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:
@@ -479,7 +478,7 @@ process diffPeaks {
}
// Collect Software Versions and references
-process softwareReport {
+process softwareVersions {
input:
@@ -502,10 +501,8 @@ process softwareReport {
file('*_mqc.txt') into softwareReferences
script:
-
"""
python3 $baseDir/scripts/generate_versions.py -o software_versions
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
"""
-
}
--
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