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Check for sample IDs characters in samplesheet and report line numbers when erroring #371

Merged
merged 3 commits into from
Jul 4, 2024
Merged

Check for sample IDs characters in samplesheet and report line numbers when erroring #371

merged 3 commits into from
Jul 4, 2024

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JoseEspinosa
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Fixes #338
Closes #370

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Jul 4, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 50f1b0d

+| ✅ 220 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-04 11:16:54

maxulysse
maxulysse reviewed Jul 4, 2024
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CHANGELOG.md
Comment on lines +15 to +16
- [[#338](https://github.com/nf-core/atacseq/issues/338)] - Check that samplesheet samples IDs do only have alphanumeric characters, dots, dashes or underscores.
- [[#370](https://github.com/nf-core/atacseq/issues/370)] - Adding line numbers to errors messages in `bin/check_samplesheet.py`
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so you link issues and not PRs?

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Both, if you look to the rnaseq changelog you also do 😉

maxulysse
maxulysse approved these changes Jul 4, 2024
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LGTM.
What's the plan towards switching to nf-validation/nf-schema?

@JoseEspinosa
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LGTM. What's the plan towards switching to nf-validation/nf-schema?

We are doing some validations inside the samplesheet apart from the normal ones. But I was discussing with @mirpedrol and @bjlang and we might give it a try for the release we are planning. We probably will start with nf-core/chipseq since there the controls are mandatory and makes it easier to implement

@JoseEspinosa JoseEspinosa merged commit a238997 into nf-core:dev Jul 4, 2024
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@JoseEspinosa JoseEspinosa mentioned this pull request Jul 5, 2024
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@JoseEspinosa JoseEspinosa mentioned this pull request Jul 19, 2024
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@maxulysse maxulysse maxulysse approved these changes

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@JoseEspinosa @maxulysse