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Merged
merged 6 commits into from
Apr 3, 2023
Merged

Prodigal update #253

merged 6 commits into from
Apr 3, 2023

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jasmezz
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@jasmezz jasmezz commented Mar 29, 2023

Closes #250

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/funcscan 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>).
  • 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).

@jasmezz jasmezz changed the base branch from master to dev March 29, 2023 13:31
@jasmezz jasmezz requested a review from a team March 29, 2023 13:34
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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 @jasmezz,

It looks like this pull-request is has been made against the nf-core/funcscan 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/funcscan 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!

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github-actions bot commented Mar 29, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e7166d

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-04-03 15:30:03

louperelo
louperelo reviewed Mar 30, 2023
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The PRODIGAL_GBK unzip might be unnecessary, otherwise this looks good to me.

jasmezz
jasmezz commented Apr 3, 2023
View reviewed changes
@jasmezz jasmezz merged commit 66b9a11 into dev Apr 3, 2023
@jasmezz jasmezz deleted the prodigal-update branch April 3, 2023 15:27
@jasmezz jasmezz mentioned this pull request Apr 26, 2023
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Update prodigal
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@jasmezz @louperelo