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Add shiftfasta #354

Merged
merged 9 commits into from
May 29, 2023
Merged

Add shiftfasta #354

merged 9 commits into from
May 29, 2023

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ramprasadn
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@ramprasadn ramprasadn commented May 26, 2023 •
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PR checklist

This PR

  • removes parameters related to shifted mitochondrial reference

  • adds GATK's ShiftFasta so that all the reference files necessary for the mitochondrial analysis can be generated by the pipeline itself.

  • 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).

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github-actions bot commented May 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 48af7d5

+| ✅ 154 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 2.8
  • Run at 2023-05-29 08:42:55

@ramprasadn ramprasadn marked this pull request as ready for review May 29, 2023 08:59
@ramprasadn ramprasadn requested review from jemten and Lucpen May 29, 2023 08:59
Lucpen
Lucpen approved these changes May 29, 2023
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CHANGELOG.md Show resolved Hide resolved
@ramprasadn ramprasadn merged commit ced4ee8 into nf-core:devplaceholder May 29, 2023
@ramprasadn ramprasadn deleted the add-shiftfasta branch June 22, 2023 15:17
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@Lucpen Lucpen Lucpen approved these changes

@jemten jemten Awaiting requested review from jemten

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@ramprasadn @Lucpen