Commit a069f6ac authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

change rule htseq to use conda virtual environment

parent 1df37222
......@@ -225,15 +225,15 @@ rule htseq:
params: library_type=config["library-type"]
conda: "CONDA/rnaSeqQuantif.yml"
shell: """
if [ $library_type = "fr-secondstrand" ]
if [ {params.library_type} = "fr-secondstrand" ]
then
strand="reverse"
elif [ $library-type = "fr-firststrand" ]
strand="yes"
htseq-count -s reverse -f bam {input} {GTF} > {output}
elif [ {params.library_type} = "fr-firststrand" ]
then
htseq-count -s yes -f bam {input} {GTF} > {output}
else
strand="no"
htseq-count -s no -f bam {input} {GTF} > {output}
fi
htseq-count -s {strand} -f bam {input} {GTF} > {output}
"""
rule deseq2_conditions:
......
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