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FEAT: Improve schema usage for input #1243

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merged 2 commits into from
Sep 18, 2023
Merged

FEAT: Improve schema usage for input #1243

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ebf0897
improve schema json for input
maxulysse Sep 18, 2023
b1407ba
update CHANGELOG
maxulysse Sep 18, 2023
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1 change: 0 additions & 1 deletion .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,5 @@ lint:
- docs/images/nf-core-sarek_logo_light.png
- lib/NfcoreTemplate.groovy
- lib/NfcoreSchema.groovy
schema_params: False
template_strings: False
multiqc_config: False
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Changed

- [#1243](https://github.com/nf-core/sarek/pull/1243) - Improve json schema usage for input

### Fixed

- [#1232](https://github.com/nf-core/sarek/pull/1232) - Fix Zenodo IDs in manifest
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18 changes: 5 additions & 13 deletions nextflow_schema.json
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Expand Up @@ -18,19 +18,11 @@
"help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory. If no input should be supplied, i.e. when --step is supplied or --build_from_index, then set --input false",
"fa_icon": "fas fa-file-csv",
"schema": "assets/schema_input.json",
"anyOf": [
{
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$"
},
{
"type": "boolean",
"enum": ["false"]
}
Comment on lines -29 to -32
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wasn't this done so --step would work without input?

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just tried it locally with:

nextflow run . -profile test,docker --outdir results

followed by:

nextflow run . -profile test,docker --outdir results --input false --step recalibrate

and it worked without failures.

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Originally yes, but we fixed it in nf-validation, now parameters evaluating to false are not validated

]
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$"
},
"input_restart": {
"type": "string",
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