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Make stringtie/merge arguments configurable (#2049)

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Added $args to command line and made using a reference annotation optional.

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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Benedetto Polimeni 2022-09-26 15:26:53 +02:00 committed by GitHub
parent 72adfbff72
commit 29568f72ca
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1 changed files with 5 additions and 3 deletions
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modules/stringtie/merge/main.nf
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@ -19,12 +19,14 @@ process STRINGTIE_MERGE {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def reference = annotation_gtf ? "-G $annotation_gtf" : ""
""" """
stringtie \\ stringtie \\
--merge $stringtie_gtf \\ --merge $stringtie_gtf \\
-G $annotation_gtf \\ $reference \\
-o stringtie.merged.gtf -o stringtie.merged.gtf \\
$args
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":