update reference.

workflow/main.nf

@@ -98,8 +98,7 @@ skipMotif = params.skipMotif
 skipPlotProfile = params.skipPlotProfile
 references = params.references
 multiqc = params.multiqc
-gtfFile_plotProfile = Channel.fromPath(params.gtf)
-gtfFile_annotPeaks = Channel.fromPath(params.gtf)
+gtfFile = Channel.fromPath(params.gtf)
 geneNames = Channel.fromPath(params.geneNames)
 
 // Check design file for errors
@@ -485,7 +484,6 @@ process plotProfile {
   input:
 
   file ("*.pooled.fc_signal.bw") from bigwigs.collect()
-  file gtf from gtfFile_plotProfile
 
   output:
 
@@ -498,7 +496,7 @@ process plotProfile {
   script:
   """
   module load deeptools/2.5.0.1
-  bash $baseDir/scripts/plot_profile.sh
+  bash $baseDir/scripts/plot_profile.sh $gtfFile
   """
 }
 
@@ -540,7 +538,6 @@ process peakAnnotation {
   input:
 
   file designAnnotatePeaks
-  file gtf from gtfFile_annotPeaks
   file geneNames
 
   output:
@@ -552,7 +549,7 @@ process peakAnnotation {
 
   """
   module load R/3.3.2-gccmkl
-  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtf $geneNames
+  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtfFile $geneNames
   """
 
 }