Refactor netmhcpan CI to use shared nf-test action#328
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jonasscheid merged 11 commits intodevfrom Feb 3, 2026
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- Make action inputs optional with backwards-compatible defaults - Add changed_since parameter to control --changed-since flag - Remove hardcoded --tag !netmhcpan from action (now passed via input) - Change NFT_WORKDIR to $TMPDIR for better Singularity compatibility - Simplify netmhcpan job by using shared action instead of duplicating setup Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.4.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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jonasscheid
commented
Jan 26, 2026
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…itopeprediction into refactor-netmhcpan-ci
Add CI file patterns to nf-test.config triggers so changed-since detects CI infrastructure changes as requiring a full test run. Pass tags to get-shards to match the filtered test set. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When snapshot files change, all tests should run to verify the updated expectations are correct. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
nf-test 0.9.3 --dry-run with --tag !netmhcpan always outputs "No tests to execute" even when tests are found. Remove tags from get-shards (matching TEMPLATE) and let the actual nf-test job handle tag filtering. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
nf-test 0.9.3 does not support tag negation with ! prefix. Remove tag "pipeline" from netmhcpan test so --tag pipeline in the main nf-test job selects all tests except netmhcpan. The netmhcpan job already uses --tag netmhcpan for positive match. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
jonasscheid
commented
Jan 27, 2026
jonasscheid
changed the title
11 tasks
axelwalter
approved these changes
Feb 3, 2026
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Refactor netmhcpan CI
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).