modify template to use nf-validation plugin #1771
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<3 |
Codecov Report
@@ Coverage Diff @@
## dev #1771 +/- ##
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- Coverage 72.93% 72.75% -0.18%
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Files 77 77
Lines 8446 8446
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- Hits 6160 6145 -15
- Misses 2286 2301 +15
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| @@ -11,6 +11,8 @@ | |||
| - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286) | |||
| - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287) | |||
| - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291)) | |||
| - Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/)) | |||
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| - Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/)) | |
| - Remove schema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/)) |
| // Schema validation default options | ||
| validationFailUnrecognisedParams = false | ||
| validationLenientMode = false | ||
| validate_params = true |
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Should we also make them camel-case?
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I'm doubting with validate_params. For schema_ignore_params you are right, it should be camelCase as it's part of the nf-validation plugin. But validate_params is only used in nf-core pipelines, so I think it should be snake_case?
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if it's params, then snake_case
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Unfortunately the nf-validation plugin is using camelCase as nextflow uses this notation, and it's ment to be for all NF pipelines and not only nf-core.
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Good point, then ok for camelCase
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Converting it to a draft again as, after some Slack discussions, we've decided to not include |
…link from singularity to apptainer on the system.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
… to Version 2.9dev.
…n showing it separately.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
…onal for Tower downloads. Given that there is the option to provide the list of remote containers to skip their download, I agree that this is reasonable.
…revisions may also be branches. Therefore, I rewrote this function to account for revisions that are not releases.
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I messed up this PR too much, so I've decided to open a new one #2300 |
Closes #1543
The validation of nextflow_schema.json files from nf-core pipelines is now part of a core Nextflow plugin: nextflow-io/nf-validation#5
Test in nf-core/testpipeline
Functions can be imported to a pipeline with
include { paramsHelp, paramsSummaryMap, paramsSummaryLog } from 'plugin/nf-validation'Schema validation code from the pipeline template
NfcoreSchema.groovyandMainWorkflow.groovyis removed.Validate a sample sheet with a JSON schema and create a channel from it. Replaces
check_samplesheetsubworkflow and code.PR checklist
CHANGELOG.mdis updateddocsis updated