From cde5c10afe7bd1255fad09f20a7b6017828b6abe Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 6 Jan 2019 16:32:25 -0600
Subject: [PATCH] fix missing genome params and annotate peaks syntax.
---
workflow/main.nf | 1 +
workflow/scripts/annotate_peaks.R | 8 ++++----
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 1103db0..bdaaa92 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -38,6 +38,7 @@ readsList = Channel
pairedEnd = params.pairedEnd
designFile = params.designFile
genomeSize = params.genomeSize
+genome = params.genome
chromSizes = params.chromSizes
fasta = params.fasta
cutoffRatio = params.cutoffRatio
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 98bb8bd..3629c4a 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -21,16 +21,16 @@ if (length(args) != 2) {
}
design_file <- args[1]
-genome <-args[2]
+genome_assembly <- args[2]
# Load UCSC Known Genes
-if(genome=='GRCh37') {
+if(genome_assembly=='GRCh37') {
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
annodb <- 'org.Hs.eg.db'
-} else if(genome=='GRCm38') {
+} else if(genome_assembly=='GRCm38') {
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
annodb <- 'org.Mm.eg.db'
-} else if(genome=='GRCh38') {
+} else if(genome_assembly=='GRCh38') {
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
annodb <- 'org.Hs.eg.db'
}
--
GitLab