Update abricate to fix inconsistent report contents #479
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jasmezz
approved these changes
May 27, 2025
jasmezz
requested changes
May 27, 2025
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Oh wait I take that back – some tests fail due to the abricate update – file name clash because of the naming check within the module. I should have asked that before you merged the abricate update, but why don't we only symlink if the file name is different than the sample name, otherwise do nothing? Right now after the if ("${assembly}" == "${prefix}.fasta") an error is triggered.
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Yeah I realised that behaviour would also break our desired behaviour (having to add a prefix) 😓 Suggestion here to only symlink when not the same: nf-core/modules#8555 |
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I think that's working now @jasmezz |
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Re-running CI checks once more: There is actually one pipeline-level nf-test snapshot that was affected by the update of abricate results. (The others not because they use |
jasmezz
approved these changes
May 27, 2025
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Than kyou @jasmezz ! |
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This ensures the sample IDs in the abricate run header matches our sample IDs, rather than the file name (which can be something different if no gunzipping has been performed on it)
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).