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Bbnorm minid #282

Merged
merged 6 commits into from
Apr 10, 2024
Merged

Bbnorm minid #282

merged 6 commits into from
Apr 10, 2024

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danilodileo
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@danilodileo danilodileo commented Apr 9, 2024 •
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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/metatdenovo 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

I am addressing the issue #280 by adding minid as parameter to bbmap_align

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github-actions bot commented Apr 9, 2024

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 @danilodileo,

It looks like this pull-request is has been made against the danilodileo/metatdenovo 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 danilodileo/metatdenovo 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 Apr 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 02d8673

+| ✅ 180 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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.
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-10 07:04:21

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github-actions bot commented Apr 9, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 98fc388

+| ✅ 179 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.1
  • 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.
  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-09 09:32:26

@danilodileo danilodileo changed the base branch from master to dev April 9, 2024 09:33
erikrikarddaniel
erikrikarddaniel reviewed Apr 9, 2024
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You forgot the changelog.

One discussion point: With a default of 0.9 we're quite a bit from the behaviour in earlier versions. Maybe that's good, but I think it should be pointed out in the CHANGELOG.md. Or we settle for a default of 0.76 which is what is the default for the tool. I think I vote for 0.9 + changelog message.

CHANGELOG.md Outdated
@@ -3,10 +3,11 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.1.0 - [date]
## v1.1.0 - [2024-04-09]
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We're not releasing today, are we? I think the version should say 1.1.0dev until we're really ready to release. There's a tool in nf-core to bump the version -- it's updated in 6-7 places.

erikrikarddaniel
erikrikarddaniel approved these changes Apr 10, 2024
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One suggestion, otherwise lgtm.

CHANGELOG.md Outdated Show resolved Hide resolved
@danilodileo @erikrikarddaniel
Update CHANGELOG.md
02d8673 
Co-authored-by: Daniel Lundin <[email protected]>
@danilodileo danilodileo merged commit 15f0995 into nf-core:dev Apr 10, 2024
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@danilodileo danilodileo mentioned this pull request Apr 10, 2024
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@danilodileo danilodileo deleted the bbnorm-minid branch April 10, 2024 08:55
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel