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nf-core subworkflows lint issue with no emit statements

Open maxulysse opened this issue 1 year ago • 2 comments

Description of the bug

cf discussion in https://nfcore.slack.com/archives/CE6PELWR4/p1705575911588159

When a subworkflow has no emit statement, the linting is failing:

╭─ [✗] 1 Subworkflow Test Failed ──────────────────────────────────────────────╮
│                          ╷                        ╷                          │
│ Subworkflow name         │ File path              │ Test message             │
│╶─────────────────────────┼────────────────────────┼─────────────────────────╴│
│ utils_nextflow_pipeline  │ subworkflows/nf-core/… │ No workflow 'emit' block │
│                          │                        │ found                    │
│                          ╵                        ╵                          │
╰──────────────────────────────────────────────────────────────────────────────╯

That being said, this should be the exception rather than the rule, but there should be ways to deal with that properly

Command used and terminal output

No response

System information

No response

maxulysse avatar Jan 19 '24 11:01 maxulysse

cf https://github.com/nf-core/modules/pull/4774

maxulysse avatar Jan 19 '24 11:01 maxulysse

Temporary fix I introduced involved using a dummy_emit option in the emit statement that can be removed when we have a better solution: https://github.com/nf-core/modules/pull/4774/commits/30ae007e717049ea273590597cb2a6ca3ffa465e

drpatelh avatar Jan 19 '24 11:01 drpatelh