nf-core subworkflows lint isn't comparing output channels between the main.nf and meta.yml
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bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
For example, nf-core subworkflows lint bcl_demultiplex passes, even though the versions channel is listed in the meta.yml but doesn't exist in the main.nf
Command used and terminal output
nf-core subworkflows lint bcl_demultiplex
INFO Linting subworkflow: 'bcl_demultiplex'
╭─ [!] 4 Subworkflow Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Subworkflow name │ File path │ Test message │
│╶─────────────────┼──────────────────────────────────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────╴│
│ bcl_demultiplex │ subworkflows/nf-core/bcl_demultiplex/main.nf │ main_nf_include_versions: Included component 'BCL2FASTQ' versions are not added │
│ │ │ in main.nf. Can be ignored if the module is using topic channels │
│ bcl_demultiplex │ subworkflows/nf-core/bcl_demultiplex/main.nf │ main_nf_include_versions: Included component 'BCLCONVERT' versions are not │
│ │ │ added in main.nf. Can be ignored if the module is using topic channels │
│ bcl_demultiplex │ subworkflows/nf-core/bcl_demultiplex/main.nf │ main_nf_version_emitted: Subworkflow does not emit software version. Can be │
│ │ │ ignored if the subworkflow is using topic channels │
│ bcl_demultiplex │ subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap │ test_snap_versions: versions not found in snapshot file. Can be ignored if the │
│ │ │ subworkflow is using topic channels │
│ ╵ ╵ │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 25 Tests Passed │
│ [!] 4 Test Warnings │
│ [✗] 0 Tests Failed │
╰───────────────────────╯
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Open a pull request that references the issue number.
Research direction
Reproduce the issue with nf-core subworkflows lint bcl_demultiplex, then compare the versions channel in subworkflows/nf-core/bcl_demultiplex/main.nf with its declaration in meta.yml. Trace the subworkflow lint checks and add coverage for mismatched output channels; done means the example no longer passes silently and the relevant lint test reports the discrepancy.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- testing-qa, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100