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handle type for val in topics correctly#3991

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mashehu merged 6 commits intonf-core:devfrom
mashehu:fix-val-as-topic
Jan 30, 2026
Merged

handle type for val in topics correctly#3991
mashehu merged 6 commits intonf-core:devfrom
mashehu:fix-val-as-topic

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@mashehu
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@mashehu mashehu commented Jan 21, 2026

Closes #3985

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codecov Bot commented Jan 21, 2026 •
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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.67%. Comparing base (2ef9d0f) to head (b698d1e).
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@prototaxites
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prototaxites commented Jan 21, 2026

Works for fastk/fastk, but something is failing after running --fix with merquryfk/merquryfk:

Fixed section of meta.yml:

  versions_merquryfk:
    - - ${task.process}:
          type: string
          description: Name of the process
      - merquryfk:
          type: string
          description: The name of the tool
      - "1.2":
          type: string
          description: The expression to obtain the version of the tool
  versions_fastk:
    - - ${task.process}:
          type: string
          description: Name of the process
      - fastk:
          type: string
          description: Name of the tool
      - "1.2":
          type: string
          description: The expression to obtain the version of the tool
  versions_r:
    - - ${task.process}:
          type: string
          description: Name of the process
      - R:
          type: string
          description: Name of the tool
      - R --version | sed "1!d; s/.*version //; s/ .*//":
          type: eval
          description: The expression to obtain the version of the tool
topics:
  versions:
    - - ${task.process}:
          type: string
          description: Name of the process
      - merquryfk:
          type: string
          description: The name of the tool
      - "1.2":
          type: string
          description: The expression to obtain the version of the tool
    - - ${task.process}:
          type: string
          description: Name of the process
      - fastk:
          type: string
          description: Name of the tool
      - "1.2":
          type: string
          description: The expression to obtain the version of the tool
    - - ${task.process}:
          type: string
          description: Name of the process
      - R:
          type: string
          description: Name of the tool
      - R --version | sed "1!d; s/.*version //; s/ .*//":
          type: eval
          description: The expression to obtain the version of the tool

lint fix output:

~/P/modules merqury_versions• 4.1s | 1 ❱ uvx --from git+https://github.com/mashehu/tools.git@fix-val-as-topic nf-core m lint merquryfk/merquryfk --fix  (nextflow)


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.6.0.dev0 - https://nf-co.re


INFO     Linting modules repo: '.'
INFO     Linting module: 'merquryfk/merquryfk'
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 1 » merquryfk/merquryfkINFO     Adding topic metadata for '1.2' at index 2: {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}
INFO     Adding topic metadata for '1.2' at index 2: {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 1 » merquryfk/merquryfkINFO     Updating modules/nf-core/merquryfk/merquryfk/meta.yml

╭─ [!] 2 Module Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                      ╷                                             ╷                                                                                            │
│ Module name          │ File path                                   │ Test message                                                                               │
│╶─────────────────────┼─────────────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────╴│
│ merquryfk/merquryfk  │ modules/nf-core/merquryfk/merquryfk/main.nf │ container_links: Unable to connect to container registry, code:  404, url:                 │
│                      │                                             │ https://community.wave.seqera.io/library/fastk_merquryfk_r-argparse_r-cowplot_pruned:d61b1 │
│                      │                                             │ 20497d4185b                                                                                │
│ merquryfk/merquryfk  │ modules/nf-core/merquryfk/merquryfk/main.nf │ main_nf_container: Container versions do not match                                         │
│                      ╵                                             ╵                                                                                            │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 2 Module Tests Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                      ╷                                              ╷                                                                                           │
│ Module name          │ File path                                    │ Test message                                                                              │
│╶─────────────────────┼──────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────╴│
│ merquryfk/merquryfk  │ modules/nf-core/merquryfk/merquryfk/meta.yml │ correct_meta_outputs: Module meta.yml does not match main.nf. Outputs should contain:     │
│                      │                                              │ {'stats': [['meta', '${prefix}.completeness.stats']], 'bed': [['meta',                    │
│                      │                                              │ '${prefix}._only.bed']], 'assembly_qv': [['meta', '${prefix}..qv']], 'qv': [['meta',      │
│                      │                                              │ '${prefix}.qv']], 'phased_block_bed': [['meta', '${prefix}.phased_block.bed']],           │
│                      │                                              │ 'phased_block_stats': [['meta', '${prefix}.phased_block.stats']], 'images': [['meta',     │
│                      │                                              │ '*.{pdf,png}']], 'versions_merquryfk': [['${task.process}', 'merquryfk', '1.2']],         │
│                      │                                              │ 'versions_fastk': [['${task.process}', 'fastk', '1.2']], 'versions_r':                    │
│                      │                                              │ [['${task.process}', 'R', 'R --version | sed "1!d; s/.version //; s/ .//"']]} Run nf-core │
│                      │                                              │ modules lint --fix to update the meta.yml file.                                           │
│ merquryfk/merquryfk  │ modules/nf-core/merquryfk/merquryfk/meta.yml │ correct_meta_topics: Module meta.yml does not match main.nf. Topics should contain:       │
│                      │                                              │ {'versions': [['${task.process}', 'merquryfk', '1.2'], ['${task.process}', 'fastk',       │
│                      │                                              │ '1.2'], ['${task.process}', 'R', 'R --version | sed "1!d; s/.version //; s/ .//"']]} Run  │
│                      │                                              │ nf-core modules lint --fix to update the meta.yml file.                                   │
│                      ╵                                              ╵                                                                                           │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  53 Tests Passed  │
│ [!]   2 Test Warnings │
│ [✗]   2 Tests Failed  │
╰───────────────────────╯

Also, the adding metadata INFO output still says "eval":

INFO     Adding topic metadata for '1.2' at index 2: {'type': 'eval', 'description': 'The expression to obtain the version of the tool'}

@mashehu
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mashehu commented Jan 21, 2026

yes, that is fixed in #3990

mirpedrol
mirpedrol approved these changes Jan 26, 2026
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some small comments, otherwise LGTM!

Comment thread nf_core/modules/lint/__init__.py Outdated
Comment thread nf_core/modules/lint/__init__.py Outdated
Comment thread tests/modules/lint/test_meta_yml.py Outdated
@mashehu mashehu enabled auto-merge (rebase) January 29, 2026 09:15
auto-merge was automatically disabled January 29, 2026 09:22

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@mashehu mashehu merged commit abcbd7c into nf-core:dev Jan 30, 2026
114 checks passed
@mashehu mashehu deleted the fix-val-as-topic branch January 30, 2026 12:52
mashehu added a commit to mashehu/tools that referenced this pull request Mar 25, 2026
@mashehu @mirpedrol @nf-core-bot
handle type for val in topics correctly (nf-core#3991)
5ca2799 
Co-authored-by: Júlia Mir Pedrol <[email protected]>
Co-authored-by: nf-core-bot <[email protected]>
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@mirpedrol mirpedrol mirpedrol approved these changes

@prototaxites prototaxites Awaiting requested review from prototaxites

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@mashehu @prototaxites @mirpedrol @nf-core-bot