Fix UNTAR/UNZIP/EPICORE version eval crashing on compressed .d input#455
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jonasscheid merged 4 commits intoMay 22, 2026
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…ng banners (nf-core#452) Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Ngarciar24
approved these changes
May 22, 2026
| output: | ||
| tuple val(meta), path("*.d"), emit: unzipped_archive | ||
| tuple val("${task.process}"), val('7za'), eval("echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//'"), topic: versions | ||
| tuple val("${task.process}"), val('7za'), eval("7za --help 2>&1 | sed -nE 's/.*p7zip Version ([0-9.]+).*/\\1/p'"), topic: versions |
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Consider quiting after the firts match as done above: | head -n1
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With above I mean line #15 [modules/local/untar/main.nf]
Ngarciar24
approved these changes
May 22, 2026
| output: | ||
| tuple val(meta), path("*.d"), emit: unzipped_archive | ||
| tuple val("${task.process}"), val('7za'), eval("echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//'"), topic: versions | ||
| tuple val("${task.process}"), val('7za'), eval("7za --help 2>&1 | sed -nE 's/.*p7zip Version ([0-9.]+).*/\\1/p'"), topic: versions |
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With above I mean line #15 [modules/local/untar/main.nf]
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Fixes #452 —
UNTAR,UNZIPandEPICOREcaptured their tool version via anevaloutput of the formecho $(...), whose unquoted command substitution spliced parenthesis-containing version banners into thebash -cstring and aborted the process, so every compressed Bruker.dinput failed; replaced with direct command pipelines (no command substitution).PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).