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Make argument checking more strict #30

Merged
merged 1 commit into from
Nov 16, 2022
Merged

Make argument checking more strict #30

merged 1 commit into from
Nov 16, 2022

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fbdtemme
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Description

Nextflow will now throw an error instead of a warning when encountering unknown parameters in the config or on the commandline.

Note for reviewers:
CustomNFCoreSchema.groovy is exactly the same as NFCoreSchema.groovy except for 176-179. The original file was kept to keep nf-core linting happy.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@linear
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linear bot commented Nov 15, 2022

EXE-321 Make nf-core-pixelator parameter checking strict

Currently, when a user makes a typo or passes an unrecognized option the argument will be ignored.

We should make error checking strict and generate an error instead of a warning.

@fbdtemme fbdtemme requested a review from ambarrio November 15, 2022 13:01
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github-actions bot commented Nov 15, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e8cf8e5

+| ✅ 147 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  27 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in aws_test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in aws_test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in aws_test_full.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in aws_test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test_full.config: // Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: // Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: // Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_full.config: // Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_aggr.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test_aggr.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/nf-core/pixelator/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/PixelgenTechnologies/nf-core-pixelator/master/nextflow_schema.json
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-15 13:00:24

ambarrio
ambarrio reviewed Nov 16, 2022
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@ambarrio ambarrio left a comment

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Small curious comments.

lib/CustomNfCoreSchema.groovy Show resolved Hide resolved
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@fbdtemme fbdtemme merged commit d07714d into dev Nov 16, 2022
@fbdtemme fbdtemme deleted the feature/exe-321 branch November 16, 2022 12:10
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@ambarrio ambarrio ambarrio approved these changes

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@fbdtemme @ambarrio