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Add alignment via STAR + postprocessing #12

Merged
merged 16 commits into from
Feb 19, 2024
Merged

Add alignment via STAR + postprocessing #12

merged 16 commits into from
Feb 19, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 7, 2024 •
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PR to add STAR to produce both genome and transcriptome-level alignment to the workflow, using the fastq_align_star subworkflow which also gives us indexing and stats generation.

Also pulled the UMI deduplication from nf-core rna-seq, though testing will have to wait until I identify some UMI-tagged riboseq data to play with.

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).

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github-actions bot commented Feb 7, 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 base branch from master to dev February 7, 2024 10:00
@pinin4fjords pinin4fjords marked this pull request as draft February 7, 2024 10:01
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github-actions bot commented Feb 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 74fc9f3

+| ✅ 188 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  17 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: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowRiboseq.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-19 16:03:09

@pinin4fjords pinin4fjords changed the title Alignment phase Add alignment via STAR + postprocessing Feb 19, 2024
@pinin4fjords pinin4fjords marked this pull request as ready for review February 19, 2024 11:40
maxulysse
maxulysse reviewed Feb 19, 2024
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maxulysse approved these changes Feb 19, 2024
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LGTM

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit d14a8d9 into dev Feb 19, 2024
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@pinin4fjords pinin4fjords deleted the alignment_phase branch February 19, 2024 16:24
@pinin4fjords pinin4fjords linked an issue Feb 19, 2024 that may be closed by this pull request
Add alignment #14
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@pinin4fjords pinin4fjords added this to the v1.0.0 milestone Feb 19, 2024
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@maxulysse maxulysse maxulysse approved these changes

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Add alignment
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