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refactor: use nf-core modules for sratools subworkflow #89

Merged
merged 4 commits into from
May 16, 2022
Merged

refactor: use nf-core modules for sratools subworkflow #89

merged 4 commits into from
May 16, 2022

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Midnighter
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@Midnighter Midnighter commented May 12, 2022 •
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Refactor the sratools subworkflow to use the updated nf-core modules. Hopefully, this will alleviate issues with the NCBI user settings, e.g., #64, #86, and #88.

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!
  • 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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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Midnighter,

It looks like this pull-request is has been made against the nf-core/fetchngs master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/fetchngs dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@Midnighter Midnighter changed the base branch from master to dev May 12, 2022 15:59
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Every damn time 😆

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github-actions bot commented May 12, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3630eb6

+| ✅ 143 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowFetchngs.groovy

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-16 08:47:11

drpatelh
drpatelh approved these changes May 16, 2022
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LGTM! Need to update the CHANGELOG too 🚀

@Midnighter Midnighter merged commit 094f5f7 into dev May 16, 2022
@Midnighter Midnighter deleted the refactor-sra branch May 16, 2022 08:52
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@Midnighter @drpatelh