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added check for case id #357

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Merged
merged 5 commits into from
Jul 7, 2023
Merged

added check for case id #357

merged 5 commits into from
Jul 7, 2023

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@evasterviga
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@evasterviga evasterviga commented May 30, 2023 •
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Adding case id check for sample sheet

This PR contains an additional feature in bin/check_samplesgeet.py to check that a case id for each sample is present in the sample sheet. Some code for checking that the column name case_id is present was already in the script.

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/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).

@evasterviga evasterviga requested a review from sima-r May 30, 2023 08:48
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github-actions bot commented May 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 900af1b

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • 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 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-07 11:28:56

jemten
jemten reviewed May 30, 2023
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@ramprasadn ramprasadn requested a review from jemten June 22, 2023 12:31
jemten
jemten reviewed Jun 22, 2023
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Looks good. @EmmaCAndersson could you update your branch with the latest changes from the raredisease dev branch?

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ramprasadn commented Jul 6, 2023

Nice work @EmmaCAndersson! Could you also update CHANGELOG.md?

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evasterviga commented Jul 7, 2023

Nice work @EmmaCAndersson! Could you also update CHANGELOG.md?

Yes! That's done now.

ramprasadn
ramprasadn approved these changes Jul 7, 2023
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LGTM! 🚀

@evasterviga evasterviga merged commit 38e01e0 into nf-core:dev Jul 7, 2023
@ramprasadn ramprasadn mentioned this pull request Aug 1, 2023
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@ramprasadn ramprasadn ramprasadn approved these changes

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@evasterviga @ramprasadn @jemten