From bce662b7e4645170b5d943d68770a320586bb3ad Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 14:18:22 +0200
Subject: [PATCH] uscs: new test on bigwigtowig convertion
---
src/nf_modules/ucsc/main.nf | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index e88f35a2..999f55fb 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -49,10 +49,10 @@ process bigwig_to_wig {
script:
"""
-bigWigToBedGraph ${params.bigwig_to_wig} \
+bigWigToWig ${params.bigwig_to_wig} \
${bw} \
- ${bg.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.bg > ${bw.simpleName}.wig
+ ${bg.simpleName}.raw
+awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.raw > ${bw.simpleName}.wig
"""
}
@@ -74,13 +74,13 @@ process bigwig2_to_wig2 {
script:
"""
-bigWigToBedGraph ${params.bigwig_to_wig} \
+bigWigToWig ${params.bigwig_to_wig} \
${bw_a} \
- ${bw_a.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.bg > ${bw_a.simpleName}.wig
+ ${bw_a.simpleName}.raw
+awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.raw > ${bw_a.simpleName}.wig
bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_b} \
- ${bw_b.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.bg > ${bw_b.simpleName}.wig
+ ${bw_b.simpleName}.raw
+awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s span=1\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.raw > ${bw_b.simpleName}.wig
"""
}
\ No newline at end of file
--
GitLab