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update to include intervals #708

Merged
merged 3 commits into from
Aug 18, 2022
Merged

update to include intervals #708

merged 3 commits into from
Aug 18, 2022

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nickhsmith
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Update the nf-core samtools/mpileup module to include the changes to interval handling

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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 @nickhsmith,

It looks like this pull-request is has been made against the nickhsmith/sarek 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 nickhsmith/sarek 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 Aug 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fbd2a23

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.0'
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-08-18 09:05:41

asp8200
asp8200 approved these changes Aug 17, 2022
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Looks fine to me.

As you may have noticed, there is one failing test, but - as far as I can tell - that is just a test which detects that this PR is going to master and not to dev as would normally be the case.

FriederikeHanssen
FriederikeHanssen requested changes Aug 18, 2022
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Nice! Thanks a lot, would you also update the changelog please? Make a new section with release 3.0.1 and add this PR.

@FriederikeHanssen
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@nf-core-bot fix linting

@nickhsmith nickhsmith merged commit a997aa1 into nf-core:master Aug 18, 2022
@nickhsmith nickhsmith deleted the module-update-samtools-mpileup branch August 18, 2022 09:58
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@asp8200 asp8200 asp8200 approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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4 participants
@nickhsmith @FriederikeHanssen @asp8200 @nf-core-bot