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Add metaBAT2 mincontig warning #349

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merged 2 commits into from
Nov 3, 2022
Merged

Add metaBAT2 mincontig warning #349

merged 2 commits into from
Nov 3, 2022

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jfy133
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@jfy133 jfy133 commented Nov 3, 2022 •
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PR checklist

Closes #347

  • 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/mag 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).

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github-actions bot commented Nov 3, 2022

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 @jfy133,

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

@jfy133 jfy133 marked this pull request as draft November 3, 2022 12:02
@jfy133 jfy133 changed the title Maxbin mincontig Add maxbin mincontig warning Nov 3, 2022
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github-actions bot commented Nov 3, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 58bc19f

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   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 ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-03 12:07:57

@jfy133 jfy133 changed the base branch from master to dev November 3, 2022 12:05
@jfy133 jfy133 marked this pull request as ready for review November 3, 2022 12:17
d4straub
d4straub approved these changes Nov 3, 2022
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LGTM.
I just restarted the tests because they failed with a time-out, bad connectivity I guess.

@alexhbnr alexhbnr changed the title Add maxbin mincontig warning Add metaBAT2 mincontig warning Nov 3, 2022
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alexhbnr commented Nov 3, 2022

Looks good to me, too.

@jfy133 jfy133 merged commit 06439ca into dev Nov 3, 2022
@jfy133 jfy133 deleted the maxbin-mincontig branch January 17, 2023 10:49
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@d4straub d4straub d4straub approved these changes

@alexhbnr alexhbnr alexhbnr approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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Successfully merging this pull request may close these issues.

Set minimal contig length for metaBAT2 to 1,500 if the provided value is smaller
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@jfy133 @alexhbnr @d4straub