From ebaa85344e46ee87b03030c962cfb255b060b675 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Thu, 8 Aug 2019 08:52:50 -0500
Subject: [PATCH] Fix biohpc.config
---
workflow/conf/biohpc.config | 6 +++---
workflow/main.nf | 2 +-
workflow/scripts/annotate_peaks.R | 9 ++++-----
3 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 980ab7b..b213558 100644
--- a/workflow/conf/biohpc.config
+++ b/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'
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index 324b14a..f654471 100644
--- a/workflow/main.nf
+++ b/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
"""
}
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 09919f0..853f7aa 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/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)
--
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