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Verified Commit 9f7c81b7 authored by Laurent Modolo's avatar Laurent Modolo
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ucsc: fix var name in bigwig_to_wig

parent 1faa76ad
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...@@ -42,7 +42,7 @@ process bigwig_to_wig { ...@@ -42,7 +42,7 @@ process bigwig_to_wig {
} }
input: input:
tuple val(file_id) path(bg) tuple val(file_id) path(bw)
output: output:
tuple val(file_id), path("*.wig"), emit: wig tuple val(file_id), path("*.wig"), emit: wig
...@@ -50,9 +50,9 @@ process bigwig_to_wig { ...@@ -50,9 +50,9 @@ process bigwig_to_wig {
script: script:
""" """
bigWigToBedGraph ${params.bigwig_to_wig} \ bigWigToBedGraph ${params.bigwig_to_wig} \
${bg} \ ${bw} \
${bg.simpleName}.bg ${bg.simpleName}.bg
awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bg.simpleName}.bg > ${bg.simpleName}.wig awk '{if(NR>1) {if(\$1!=lastChrom){printf("variableStep chrom=%s\\n",\$1);lastChrom=\$1;}print \$2,\$4}}' ${bw.simpleName}.bg > ${bw.simpleName}.wig
""" """
} }
......
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