nf-core / nf-core/tools

nf-core subworkflows lint issue with no emit statements

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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

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

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the Python linting check that emits the “No workflow 'emit' block found” message for nf-core subworkflows, then reproduce the failure with a subworkflow that has no emit statement. Done means valid no-emit subworkflows are handled without a false lint failure while the usual emit validation remains intact.

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
35/100

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