Commit 072f65f0 authored by Philippe BORDRON's avatar Philippe BORDRON
Browse files

Merge branch 'master' into gsea-fix

parents 94cb8844 4e1d9071
......@@ -30,3 +30,4 @@ dependencies:
- r-curl
- r-rcpp
- r-openssl
- r-foreign
......@@ -399,11 +399,11 @@ rule unknown_index:
input:
unknown = MAINDIR+"/unknown.fastq.gz"
output:
count = MAINDIR+"/unknown_indexes.count"
counts = MAINDIR+"/unknown_indexes.count"
params:
tmpdir = MAINDIR
shell:
"gunzip -c {input.unknown} | awk 'NR%4==1' | cut -d\":\" -f8 | cut -c 1-6 | LC_ALL=C sort -T {params.tmpdir} | uniq -c | sed -e 's/^[ ]*//' | sort -k1,1nr > {output.count}"
"gunzip -c {input.unknown} | awk 'NR%4==1' | cut -d\":\" -f8 | cut -c 1-6 | LC_ALL=C sort -T {params.tmpdir} | uniq -c | sed -e 's/^[ ]*//' | sort -k1,1nr > {output.counts}"
rule count:
input:
......
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