feat(maltextract): add stub block and migrate to topic channel versions#11419
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HReed1 wants to merge 10 commits intonf-core:masterfrom
Open
feat(maltextract): add stub block and migrate to topic channel versions#11419HReed1 wants to merge 10 commits intonf-core:masterfrom
HReed1 wants to merge 10 commits intonf-core:masterfrom
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- Replace versions.yml / END_VERSIONS with topic channel emit (versions_maltextract) - Version eval: MaltExtract --help | head -n 2 | tail -n 1 | sed - Add stub block: mkdir -p results - Update tests: sanitizeOutput on both tests, add stub test case - Remove legacy versions output block from meta.yml Contributes to nf-core#4570
…t assertions to avoid empty file md5 lint failure
… channel assert
Previous snap was missing the 'versions' named snapshot required by
snapshot(process.out.versions_maltextract).match('versions'). This caused
'snapshot with id versions not found' in CI mode.
Re-ran nf-test --update-snapshot to add the versions key.
…ion causing shard 4 failure
…st_snap_versions check
…nap_versions check
SPPearce
reviewed
Apr 30, 2026
| 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)
Suggested change
| { 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 |
Contributor
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This probably needs to be
Suggested change
| process.out.versions_maltextract | |
| process.out.findAll { key, val -> key.startsWith('versions') }) |
to pass linting.
SPPearce
reviewed
Apr 30, 2026
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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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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.