Commit 7c9b59d2 authored by Damien VINTACHE's avatar Damien VINTACHE
Browse files

ajout de l'environnement CONDA/rnaSeqQuantif.yml pour la règle buildReport

parent 1b97d658
......@@ -234,10 +234,10 @@ rule htseq:
shell: """
if [ {params.library_type} = "reverse" ]
then
htseq-count -s reverse -f bam {input} {GTF} > {output}
htseq-count -s reverse -f bam {input} {GTF} > {output}
elif [ {params.library_type} = "yes" ]
then
htseq-count -s yes -f bam {input} {GTF} > {output}
htseq-count -s yes -f bam {input} {GTF} > {output}
else
htseq-count -s no -f bam {input} {GTF} > {output}
fi
......@@ -283,8 +283,8 @@ rule buildReport:
input:
expand(OUTPUTDIR+"/DESEQ2/results/{suffixe}",suffixe=["NormalizedCountMatrix.txt","NormalizedCountMatrixFiltered.txt","PCAplot.png","sampletosampledistance.jpeg"]),
OUTPUTDIR+"/Report/TEMPLATE/templateCopied.txt"
output:
report = OUTPUTDIR+"/Report/report.html",
output: report = OUTPUTDIR+"/Report/report.html"
conda: "CONDA/rnaSeqQuantif.yml"
shell:
"""
python {SNAKEFILEDIR}/scripts/make_html.py -c {config[conff]} -s {config[projf]} -t {SNAKEFILEDIR}/TEMPLATE/index.html -o {output.report}
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment