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Add alignment based quantification with Salmon #42

Merged
merged 6 commits into from
Apr 8, 2024
Merged

Add alignment based quantification with Salmon #42

merged 6 commits into from
Apr 8, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Apr 5, 2024 •
edited

Add alignment-based quantification with Salmon based on what's done in the rnaseq workflow.

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/riboseq 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).

@pinin4fjords pinin4fjords changed the base branch from master to dev April 5, 2024 09:37
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github-actions bot commented Apr 5, 2024

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/riboseq 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/riboseq 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 title Readd quantification Add alignment based quantification with Salmon Apr 5, 2024
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github-actions bot commented Apr 5, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5560996

+| ✅ 186 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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!
  • schema_description - No description provided in schema for parameter: skip_ribotricer

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-08 15:11:37

maxulysse
maxulysse reviewed Apr 8, 2024
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Update CHANGELOG.md
5560996 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
maxulysse
maxulysse approved these changes Apr 8, 2024
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LGTM

@pinin4fjords pinin4fjords merged commit fda4028 into dev Apr 8, 2024
17 checks passed
@pinin4fjords pinin4fjords deleted the readd_quantification branch April 8, 2024 15:41
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@maxulysse maxulysse maxulysse approved these changes

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