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Sortmerna: index once #35

Merged
merged 14 commits into from
Feb 27, 2024
Merged

Sortmerna: index once #35

merged 14 commits into from
Feb 27, 2024

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pinin4fjords
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I got bored of the existing sortmerna setup, where rRNA reference indexing was happening within every run (about 10 minutes each).

This PR changes sortmerna usage to mirror that of other alignment-based methodlogies (hisat2, bbsplit etc), by indexing once in the 'prepare_genome' step and passing that index to the alignment/ run phase.

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 27, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 079676b

+| ✅ 184 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  18 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 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!
  • 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 2.13
  • Run at 2024-02-27 09:33:39

@maxulysse
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cf: nf-core/references#16

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit 2777636 into dev Feb 27, 2024
85 checks passed
@pinin4fjords pinin4fjords deleted the sortmerna_index_once branch February 27, 2024 14:51
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@maxulysse maxulysse maxulysse approved these changes

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