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bismark/report: allow missing input data (#400)

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* bismark/report: allow missing data

* bismark/summary: improve matching of process output
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Patrick Hüther 2021-04-06 11:59:00 +02:00 committed by GitHub
parent 4a1571317d
commit 6c70d65ae6
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2 changed files with 5 additions and 9 deletions
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8
software/bismark/report/main.nf
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@ -22,17 +22,13 @@ process BISMARK_REPORT {
tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
output: output:
tuple val(meta), path("*{html,txt}"), emit: report tuple val(meta), path("*report.{html,txt}"), emit: report
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
""" """
bismark2report \\ bismark2report $options.args
--alignment_report $align_report \\
--dedup_report $dedup_report \\
--splitting_report $splitting_report \\
--mbias_report $mbias
echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
""" """

2
software/bismark/summary/main.nf
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@ -25,7 +25,7 @@ process BISMARK_SUMMARY {
path(mbias) path(mbias)
output: output:
path("*{html,txt}") , emit: summary path "*report.{html,txt}", emit: summary
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script: