From 5f001abba3c17d192a2eb3d8d98397a1d8d0bc2c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Oct 2021 14:10:08 +0200
Subject: [PATCH] ucsc: add span info
---
src/nf_modules/ucsc/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index fefde335..e88f35a2 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -52,7 +52,7 @@ process bigwig_to_wig {
bigWigToBedGraph ${params.bigwig_to_wig} \
${bw} \
${bg.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.bg > ${bw.simpleName}.wig
+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
"""
}
@@ -77,10 +77,10 @@ process bigwig2_to_wig2 {
bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_a} \
${bw_a.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_a.simpleName}.bg > ${bw_a.simpleName}.wig
+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
bigWigToBedGraph ${params.bigwig_to_wig} \
${bw_b} \
${bw_b.simpleName}.bg
-awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw_b.simpleName}.bg > ${bw_b.simpleName}.wig
+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
"""
}
\ No newline at end of file
--
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