Fix biohpc.config

workflow/conf/biohpc.config

@@ -78,7 +78,7 @@ params {
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh38/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/human/GRCh38/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.gtf'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
     }
     'GRCh37' {
@@ -86,7 +86,7 @@ params {
       genomesize = 'hs'
       chromsizes = '/project/shared/bicf_workflow_ref/human/GRCh37/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/human/GRCh37/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.gtf'
+      gtf = '/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt'
     }
     'GRCm38' {
@@ -94,7 +94,7 @@ params {
       genomesize = 'mm'
       chromsizes = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genomefile.txt'
       fasta = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genome.fa'
-      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.gtf'
+      gtf = '/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf'
       geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
     }
   }

workflow/main.nf

@@ -552,7 +552,7 @@ process peakAnnotation {
 
   """
   module load R/3.3.2-gccmkl
-  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $genome $gtf $geneNames
+  Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $gtf $geneNames
   """
 
 }

workflow/scripts/annotate_peaks.R

@@ -16,14 +16,13 @@ library(GenomicFeatures)
 args <- commandArgs(trailingOnly=TRUE)
 
 # Check input args
-if (length(args) != 4) {
-  stop("Usage: annotate_peaks.R annotate_design.tsv genome_assembly gtf geneNames", call.=FALSE)
+if (length(args) != 3) {
+  stop("Usage: annotate_peaks.R annotate_design.tsv gtf geneNames", call.=FALSE)
 }
 
 design_file <- args[1]
-genome_assembly <- args[2]
-gtf <- args[3]
-geneNames <- args[4]
+gtf <- args[2]
+geneNames <- args[3]
 
 # Load UCSC Known Genes
 txdb <- makeTxDbFromGFF(gtf)