feat(maltextract): add stub block and migrate to topic channel versions#11419
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| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(sanitizeOutput(process.out)).match() }, | ||
| { assert snapshot(process.out.versions_maltextract).match("versions") } |
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Don't need this given that process.out includes all the channels (plus we don't use more than one snapshot (a few old nf-tests do, but they need rewriting)
| { assert snapshot(process.out.versions_maltextract).match("versions") } |
| path("${process.out.results.get(0).get(1)}/ScanSummary.txt"), | ||
| path("${process.out.results.get(0).get(1)}/error.txt").text == "", | ||
| path("${process.out.results.get(0).get(1)}/log.txt"), | ||
| process.out.versions_maltextract |
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This probably needs to be
| process.out.versions_maltextract | |
| process.out.findAll { key, val -> key.startsWith('versions') }) |
to pass linting.
SPPearce
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A few comments, but mostly there are unrelated changes that shouldn't be part of this PR
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@SPPearce — Spot on! That branch had somehow picked up a ton of divergence and unrelated files (including that ectyper file). I've nuked the old branch, pulled a clean branch off upstream/master, and re-committed the maltextract migration atomically. While I was in there, I stripped out the // meta map anti-pattern and the redundant versions snapshot assertion, relying solely on sanitizeOutput() now. I also fixed a cross-runner determinism issue where log.txt was failing MD5 checks on Conda/Docker CI runners due to execution timestamps and environment paths. It now correctly snapshots the file name to assert existence without hashing the volatile log contents. It's passing nf-test and 53/53 lint checks locally. Ready for another look! |
…ns (nf-core#11419) feat(maltextract): migrate to topic channel versions and add stub
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Contribution to #4570 — Stub+Topic Channel Migration
Migrates
maltextractto the nf-core v4.0.1 topic channel versioning standard and adds a stub block.Changes
main.nf: Replacedversions.yml/END_VERSIONSheredoc with topic channel emit (versions_maltextract). Version eval:MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//'. Addedstubblock withmkdir -p results.meta.yml: Removed legacyversions:output block; lint fixed.tests/main.nf.test: Replacedprocess.out.versionswithsanitizeOutput(process.out). Added stub test case (stub uses emptyncbi_dirinput).tests/main.nf.test.snap: Regenerated snapshots (2 created).Test results (local,
--profile docker,wave)Stability run: ✅ 2/2 passed
Part of the systematic migration tracked in #4570.