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fix: output bai from ALIGN_CONSENSUS_BAM #79

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merged 1 commit into from
Sep 24, 2024
Merged

fix: output bai from ALIGN_CONSENSUS_BAM #79

merged 1 commit into from
Sep 24, 2024

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znorgaard
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@znorgaard znorgaard commented Sep 20, 2024 •
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Closes #74.

This PR updates the modules.config files withNames for setting publishDirs to use the simple names for processes to enable users to more easily customize parameters.

It also updates the globs for bam/bais to be more concise and ouputs the bai generated during ALIGN_CONSENSUS_BAM.

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/fastquorum branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

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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 @znorgaard,

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

@znorgaard znorgaard changed the base branch from master to dev September 20, 2024 16:11
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github-actions bot commented Sep 20, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 5cdae0a

+| ✅ 180 tests passed       |+
#| ❔   8 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 19:13:35

@znorgaard znorgaard changed the title fix: output bai when using ht mode fix: output bai from ALIGN_CONSENSUS_BAM Sep 20, 2024
@znorgaard znorgaard marked this pull request as ready for review September 20, 2024 16:34
@znorgaard znorgaard requested a review from SPPearce September 20, 2024 16:34
@znorgaard znorgaard mentioned this pull request Sep 20, 2024
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SPPearce approved these changes Sep 24, 2024
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Ok, that is both explicit and compact with the patterns for the files, I like it.

@znorgaard znorgaard merged commit 811b32c into dev Sep 24, 2024
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@znorgaard znorgaard deleted the zn_output_bai branch September 24, 2024 20:03
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mapped BAM index not produced in high-throughput (ht) mode
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