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nf-core modules lint --fix produces mangled output
Description of the bug
When I use nf-core/modules lint --fix on a module PR, the resulting meta.yml does not successfully lint.
The PR where I encountered the issue: https://github.com/nf-core/modules/pull/9360
The meta.yml at time of writing: https://github.com/nf-core/modules/blob/042a85dfd3a924e299099a22b299b077d7d722a5/modules/nf-core/trident/fetch/meta.yml
Command used and terminal output
The original linting error:
╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶───────────────┼────────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ trident/fetch │ modules/nf-core/trident/fetch/meta.yml │ correct_meta_outputs: Module meta.yml does not match main.nf. Outputs should contain: {'poseidon_yml': ['output_archive//POSEIDON.yml'], │
│ │ │ 'geno': ['output_archive//.{bed'], 'snp': ['output_archive//.{bim'], 'ind': ['output_archive//.{fam'], 'janno': ['output_archive//.janno'], │
│ │ │ 'ssf': ['output_archive//.ssf'], 'bib': ['output_archive//.bib'], 'changelog': ['output_archive//CHANGELOG.md'], 'readme': │
│ │ │ ['output_archive/*/README.md'], 'versions': ['versions.yml']} Run nf-core modules lint --fix to update the meta.yml file. │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
The meta.yml created by nf-core modules lint trident/fetch --fix:
[...]
input:
- - archive_dir:
type: directory
description: |
The path to the directories containing any previously downloaded Poseidon archive files.
If this is provided, trident fetch will check these directories, and only download missing packages from the Poseidon-Framework server.
- fetch_s:
type: string
description: The fetchString provided to trident fetch (`--fetchString`),
if any.
- fetch_fn:
type: file
description: A file containing a list of fetchStrings provided to trident
fetch (`--fetchFile`), if any.
pattern: "*.txt"
ontologies: []
output:
poseidon_yml:
- output_archive/*/POSEIDON.yml:
type: file
description: The POSEIDON.yml file of any newly downloaded package(s).
pattern: "output_archive/*/POSEIDON.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
geno:
- output_archive/*/*.{bed: {}
snp:
- output_archive/*/*.{bim: {}
ind:
- output_archive/*/*.{fam: {}
janno:
- output_archive/*/*.janno:
type: file
description: The .janno annotation files of any newly downloaded
package(s).
pattern: "output_archive/*/*.janno"
ontologies: []
ssf:
- output_archive/*/*.ssf:
type: file
description: The .ssf files of any newly downloaded package(s).
pattern: "output_archive/*/*.ssf"
ontologies: []
bib:
- output_archive/*/*.bib:
type: file
description: The .bib bibliography files of any newly downloaded
package(s).
pattern: "output_archive/*/*.bib"
ontologies: []
changelog:
- output_archive/*/CHANGELOG.md:
type: file
description: The CHANGELOG.md files of any newly downloaded package(s).
pattern: "output_archive/*/CHANGELOG.md"
ontologies: []
readme:
- output_archive/*/README.md:
type: file
description: The README.md files of any newly downloaded package(s).
pattern: "output_archive/*/README.md"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: "http://edamontology.org/format_3750" # YAML
[...]
The output of nf-core modules lint trident/fetch after running with --fix:
╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶───────────────┼────────────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ trident/fetch │ modules/nf-core/trident/fetch/meta.yml │ meta_yml_valid: The meta.yml of the module trident/fetch is not valid: {'output_archive//.{bim': {}} is not valid under any of the given │
│ │ │ schemas. Check the entry for output. │
│ ╵ ╵ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
System information
Nextflow version: 25.04.8 build 5956 Hardware: MacBook Pro OS: macOS 15.4 (24E248) Version of nf-core/tools: 3.4.1 Python version: 3.14.0
can you try with the current dev version (pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev)? I think I added a fix there for this.
Sorry for the delay.
Tested today with nf-core/tools version 3.6.0.dev0, and the problem persists.
The resulting "fixed" meta looks like this:
geno:
- output_archive/*/*.{bed: {}
snp:
- output_archive/*/*.{bim: {}
ind:
- output_archive/*/*.{fam: {}