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Samplesheet versioning #121

Merged
merged 2 commits into from Dec 15, 2021
Merged

Samplesheet versioning #121

merged 2 commits into from Dec 15, 2021

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JoseEspinosa
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The samplesheet files in the test-dataset repository have been moved to a new folder to allow its versioning see here, as was discussed on #120

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/smrnaseq 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).
  • 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).

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github-actions bot commented Dec 1, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9b4d2da

+| ✅ 127 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.0.0'
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_exist - File is ignored: bin/scrape_software_versions.py
  • files_exist - File is ignored: modules/local/get_software_versions.nf
  • files_unchanged - File ignored due to lint config: .markdownlint.yml
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: bin/scrape_software_versions.py
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-12-01 10:42:22

@lpantano
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lpantano commented Dec 7, 2021

is this ready?

@JoseEspinosa
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Sorry @lpantano did not see your message... 😓
Yes, it is ready the only bit missing is that I tried to run the test_full profile and multiqc (see slack) was giving an error but otherwise, the samplesheet versioning is implemented and working. So I will now mark this PR as ready for review and we can try to solve the other issue before realising.

@JoseEspinosa JoseEspinosa marked this pull request as ready for review December 15, 2021 11:46
@lpantano lpantano merged commit 7954432 into nf-core:dev Dec 15, 2021
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@lpantano lpantano lpantano approved these changes

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@JoseEspinosa @lpantano