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switch to nf-validation for parameter and samplesheet validation#386

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ramprasadn merged 5 commits into
nf-core:devfrom
genomic-medicine-sweden:bumpversion
Jul 26, 2023
Merged

switch to nf-validation for parameter and samplesheet validation#386
ramprasadn merged 5 commits into
nf-core:devfrom
genomic-medicine-sweden:bumpversion

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@ramprasadn

@ramprasadn ramprasadn commented Jul 24, 2023 •
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PR checklist

Use nf-validation plugin for parameter and samplesheet validation

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@github-actions

github-actions Bot commented Jul 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d671af6

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-26 13:55:06

@ramprasadn ramprasadn changed the title switch to validation switch to nf-validation for parameter and samplesheet validation Jul 24, 2023
@ramprasadn ramprasadn marked this pull request as ready for review July 24, 2023 20:32
nvnieuwk
nvnieuwk approved these changes Jul 26, 2023
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@nvnieuwk nvnieuwk left a comment

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LGTM! How did the implementation go? Anything that could have been made easier? :p

@ramprasadn

ramprasadn commented Jul 26, 2023

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Fairly straightforward 😅
Only thing I found a bit confusing was navigating the website, but I noticed that was already raised on slack 😜

@ramprasadn ramprasadn merged commit 78b50c1 into nf-core:dev Jul 26, 2023
@nvnieuwk

nvnieuwk commented Jul 26, 2023

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Fairly straightforward sweat_smile Only thing I found a bit confusing was navigating the website, but I noticed that was already raised on slack stuck_out_tongue_winking_eye

Awesome thanks! Yes Phil fixed that indeed

@ramprasadn ramprasadn deleted the bumpversion branch July 26, 2023 14:21
@ramprasadn ramprasadn mentioned this pull request Aug 1, 2023
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@ramprasadn @nvnieuwk