Fix main.

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
   """
-
 }