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update mqc command

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This commit is contained in:
Matthias De Smet 2022-06-08 14:02:04 +02:00
parent 439d2a9e67
commit f1e33ca6e0
1 changed files with 7 additions and 2 deletions
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9
modules/multiqc/main.nf
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@ -8,7 +8,7 @@ process MULTIQC {
input: input:
path multiqc_files, stageAs: "?/*" path multiqc_files, stageAs: "?/*"
tuple path(mqc_config), path(mqc_logo) tuple path(multiqc_config), path(multiqc_logo)
output: output:
path "*multiqc_report.html", emit: report path "*multiqc_report.html", emit: report
@ -21,8 +21,13 @@ process MULTIQC {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def config = multiqc_config ?: '--config $multiqc_config'
""" """
multiqc -f $args . multiqc \
--force \
$config \
$args \
.
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":