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Optional-phred-scores #342

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merged 10 commits into from Apr 17, 2024
Merged

Optional-phred-scores #342

merged 10 commits into from Apr 17, 2024

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apeltzer
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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/smrnaseq 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 @apeltzer,

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

@apeltzer apeltzer changed the base branch from master to dev April 17, 2024 09:33
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github-actions bot commented Apr 17, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aecb218

+| ✅ 182 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-17 11:21:23

@apeltzer apeltzer mentioned this pull request Apr 17, 2024
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@fmalmeida fmalmeida self-requested a review April 17, 2024 10:24
fmalmeida
fmalmeida approved these changes Apr 17, 2024
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LGTM.

The .transpose() line is ensuring you have a combination, adapter+ID, for each read, right?

@apeltzer
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LGTM.

The .transpose() line is ensuring you have a combination, adapter+ID, for each read, right?

Yes exactly :) Need that for mirtrace

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Some weird CI hiccups happening now :(

@apeltzer apeltzer enabled auto-merge April 17, 2024 11:20
@apeltzer apeltzer merged commit 2741a78 into dev Apr 17, 2024
10 checks passed
@apeltzer apeltzer deleted the optional-phred-scores branch April 17, 2024 11:22
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@grst grst grst left review comments

@fmalmeida fmalmeida fmalmeida approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@apeltzer @grst @fmalmeida @FriederikeHanssen