Commit 78783fa2 authored by Philippe BORDRON's avatar Philippe BORDRON
Browse files

Merge branch 'add-param-multiqc' into 'master'

add possibility to give params to multiqc

See merge request !14
parents 0a2bc8ad 38810bff
Pipeline #31863 failed with stages
in 25 minutes and 28 seconds
......@@ -149,6 +149,9 @@
"fastqc": {
"type": "object"
},
"multiqc": {
"type": "object"
},
"quality-filter": {
"type": "object"
},
......
......@@ -707,11 +707,13 @@ rule fastqc:
rule multiqc:
input: getInput("multiqc")
output: getOutput("multiqc")
params: logfile = config["global"]["outdir"] + "/" + LOGFILE
params:
logfile = config["global"]["outdir"] + "/" + LOGFILE,
options = getOptions("multiqc")
conda: "conda/multiqc.yml"
priority: 1
shell: """
multiqc -f {outdir}/fastqc --outdir `dirname {output[0]}`
multiqc -f {outdir}/fastqc --outdir `dirname {output[0]}` {params.options}
echo "\nMultiQc.....OK" >> {params.logfile}
"""
......
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