When running nf-core modules lint --fix, data in meta.yml can be made incorrectly if things that look like inputs appear in comments. For example:
In main.nf for the busco module:
input:
tuple val(meta), path('tmp_input/*')
val mode // Required: One of genome, proteins, or transcriptome
val lineage // Required: lineage to check against, "auto" enables --auto-lineage instead
path busco_lineages_path // Recommended: path to busco lineages - downloads if not set
path config_file // Optional: busco configuration file
The // Recommended: path to busco causes the - to: {} in meta.yml:
- - busco_lineages_path:
type: directory
description: Path to local BUSCO lineages directory.
- to: {}
Which causes the following error:
╭─ [✗] 3 Module Tests Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶─────────────┼────────────────────────────────┼───────────────────────────────────────────────────────────────────────────────────────╴│
│ busco │ modules/nf-core/busco/main.nf │ Local copy of module does not match remote │
│ busco │ modules/nf-core/busco/meta.yml │ Local copy of module does not match remote │
│ busco │ modules/nf-core/busco/meta.yml │ The meta.yml of the module busco is not valid: 'type' is a required property. Check │
│ │ │ the entry for input. │
│ ╵ ╵ │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Description of the bug
When running
nf-core modules lint --fix, data inmeta.ymlcan be made incorrectly if things that look like inputs appear in comments. For example:In
main.nffor the busco module:The
// Recommended: path to buscocauses the- to: {}inmeta.yml:Which causes the following error:
Command used and terminal output
System information