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Make target bed file optional for WGS mode #395

Merged
merged 5 commits into from Aug 4, 2023
Merged

Make target bed file optional for WGS mode #395

merged 5 commits into from Aug 4, 2023

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ramprasadn
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PR checklist

Fixes #375

  • 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).

@ramprasadn ramprasadn linked an issue Aug 1, 2023 that may be closed by this pull request
Pipeline in WGS mode appears to require target_bed #375
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github-actions bot commented Aug 1, 2023 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aea0b73

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

❗ 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 2023-08-04 08:22:17

@ramprasadn ramprasadn marked this pull request as ready for review August 1, 2023 16:33
jemten
jemten approved these changes Aug 4, 2023
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good stuff

@ramprasadn ramprasadn merged commit ccd6a79 into nf-core:dev Aug 4, 2023
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@ramprasadn ramprasadn mentioned this pull request Aug 4, 2023
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@ramprasadn ramprasadn deleted the update-config branch August 22, 2023 10:37
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@jemten jemten jemten approved these changes

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Pipeline in WGS mode appears to require target_bed
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@ramprasadn @jemten