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Dragen germline topics migration #10853

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Dragen germline topics migration #10853

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5a86d2a
Migrate dragen/germline module to topic channels
DogaTestere Mar 13, 2026
f6d62c1
Merge branch 'nf-core:master' into dragen_germline_topics_migration
DogaTestere Mar 13, 2026
d5c7a96
Merge branch 'master' into dragen_germline_topics_migration
DogaTestere Mar 13, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/dragen/germline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ process DRAGEN {
path "streaming_log_*.csv" , optional: true, emit: streaming_log_csv
path "*_usage.txt" , emit: usage_txt
path "**" , emit: all
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('dragen'), eval("dragen --version 2>&1 | sed 's/^dragen Version //;s/ Hash.*//'"), emit: versions_dragen, topic: versions
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@atrigila atrigila Mar 13, 2026

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It seems that the command capturing the version is not correct. Could you modify it so that it correctly prints the version?


when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -394,22 +394,12 @@ process DRAGEN {
$format_input \\
--output-file-prefix $prefix \\
--output-directory \$(pwd)

cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragen: \$(echo \$(dragen --version 2>&1) | sed 's/^dragen Version //;s/ Hash.*//')
END_VERSIONS
"""

stub:
def VERSION = "stub"
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch 20251120_usage.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragen: ${VERSION}
END_VERSIONS
"""
}
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