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modify template to use nf-validation plugin for parameter validation #2300

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Merged
mirpedrol merged 11 commits into from
Jun 13, 2023
Merged

modify template to use nf-validation plugin for parameter validation #2300

mirpedrol merged 11 commits into from
Jun 13, 2023

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@mirpedrol
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@mirpedrol mirpedrol commented Jun 5, 2023 •
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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
Also tested with real pipelines rnaseq, funcscan and sarek.

Functions can be imported to a pipeline with include { paramsHelp, paramsSummaryMap, paramsSummaryLog } from 'plugin/nf-validation'

Schema validation code from the pipeline template NfcoreSchema.groovy and MainWorkflow.groovy is removed.

Validate a sample sheet with a JSON schema.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@mirpedrol mirpedrol mentioned this pull request Jun 5, 2023
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@mirpedrol mirpedrol changed the base branch from master to dev June 5, 2023 09:43
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codecov bot commented Jun 5, 2023 •
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Codecov Report

Merging #2300 (7af5f95) into dev (646a566) will decrease coverage by 0.04%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev    #2300      +/-   ##
==========================================
- Coverage   72.97%   72.93%   -0.04%     
==========================================
  Files          78       78              
  Lines        8732     8732              
==========================================
- Hits         6372     6369       -3     
- Misses       2360     2363       +3
Impacted Files Coverage Δ
nf_core/lint/files_exist.py 78.00% <ø> (ø)
nf_core/lint/files_unchanged.py 72.61% <ø> (ø)
nf_core/lint/nextflow_config.py 77.45% <ø> (ø)
nf_core/schema.py 78.84% <100.00%> (ø)

... and 3 files with indirect coverage changes

mirpedrol
mirpedrol commented Jun 7, 2023
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@mirpedrol mirpedrol requested a review from mashehu June 9, 2023 07:30
mashehu
mashehu approved these changes Jun 9, 2023
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mirpedrol
mirpedrol commented Jun 9, 2023
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mirpedrol
mirpedrol commented Jun 9, 2023
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mirpedrol
mirpedrol commented Jun 9, 2023
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nvnieuwk commented Jun 9, 2023

I think we should also remove the INPUT_CHECK process for the .fromSamplesheet() function?

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mirpedrol commented Jun 9, 2023

I think we should also remove the INPUT_CHECK process for the .fromSamplesheet() function?

As we don't have tooling to help create the JSON schema for a sample sheet, we thought that it would be best to not make it mandatory in the template update, and instead let it to the pipeline maintainers to decide if they want to add it or wait.

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nvnieuwk commented Jun 12, 2023

As we don't have tooling to help create the JSON schema for a sample sheet, we thought that it would be best to not make it mandatory in the template update, and instead let it to the pipeline maintainers to decide if they want to add it or wait.

Good point! Thanks for clarifying!

@mirpedrol mirpedrol merged commit 3c69971 into nf-core:dev Jun 13, 2023
@mirpedrol mirpedrol deleted the schema-validation-2 branch June 13, 2023 14:02
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Port schema validation to core Nextflow (plugin)

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