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Add missing files from Tximport processing #1302

Merged
merged 2 commits into from
May 16, 2024
Merged

Add missing files from Tximport processing #1302

merged 2 commits into from
May 16, 2024

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pinin4fjords
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Fixes #1188

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/rnaseq 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).

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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 @pinin4fjords,

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

@pinin4fjords pinin4fjords changed the base branch from master to dev May 16, 2024 14:22
@pinin4fjords pinin4fjords changed the title Tximport fix missing files Add missing files from Tximport processing May 16, 2024
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github-actions bot commented May 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1374149

+| ✅ 171 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-16 14:26:28

@pinin4fjords pinin4fjords merged commit e0b41b4 into dev May 16, 2024
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@pinin4fjords pinin4fjords mentioned this pull request May 17, 2024
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@pinin4fjords
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Turns out there were good reasons the files were missing- see #847.

Probably some tidying up in order to make it clear that there's only one abundances output.

@pinin4fjords pinin4fjords mentioned this pull request May 28, 2024
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@maxulysse maxulysse deleted the tximport_fix_missing_files branch May 29, 2024 14:48
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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Successfully merging this pull request may close these issues.

SALMON_TXIMPORT process produces two tsv files that are not marked for export
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