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Add STAR aligner #142

Merged
merged 15 commits into from
Jul 17, 2024
Merged

Add STAR aligner #142

merged 15 commits into from
Jul 17, 2024

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edmundmiller
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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/nascent 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).

@edmundmiller edmundmiller added this to the 2.3.0 milestone Apr 26, 2024
@edmundmiller edmundmiller self-assigned this Apr 26, 2024
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github-actions bot commented Apr 26, 2024 •
edited
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 4bd6a11

+| ✅ 192 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • actions_ci - '.github/workflows/ci.yml' is not triggered on expected events
  • actions_ci - Minimum pipeline NF version '23.04.0' is not tested in '.github/workflows/ci.yml'
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • 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 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!
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-17 16:09:17

@edmundmiller edmundmiller changed the base branch from master to dev April 26, 2024 01:40
@nf-core nf-core deleted a comment from github-actions bot Jul 17, 2024
maxulysse
maxulysse reviewed Jul 17, 2024
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conf/igenomes.config Outdated Show resolved Hide resolved
maxulysse
maxulysse reviewed Jul 17, 2024
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main.nf
Comment on lines 40 to +41
params.hisat2_index = getGenomeAttribute('hisat2')
params.star_index = null
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so no possible to get from igenomes, right?

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Nope, it's not up-to-date, and I wanted to use the latest version of STAR for benchmarking 😞

I have little motivation to hack around the current aws-igenomes quirks, I'd rather spend that time on nf-core/references 😉

maxulysse
maxulysse reviewed Jul 17, 2024
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workflows/nascent.nf
Comment on lines +17 to +20
include {
UNTAR as UNTAR_HISAT2_INDEX
UNTAR as UNTAR_STAR_INDEX
} from '../modules/nf-core/untar/main'
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I'd rather do 2 include statement, it reads nicer IMO

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Talk to me when someone writes a formatter 😛

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@edmundmiller edmundmiller Jul 17, 2024 •
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I like the split includes, but I'll gladly adhere to a style guide once there's a formatter that handles it for me.

maxulysse
maxulysse approved these changes Jul 17, 2024
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Minor comments

@edmundmiller edmundmiller marked this pull request as ready for review July 17, 2024 16:48
@edmundmiller edmundmiller merged commit 9561941 into dev Jul 17, 2024
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@edmundmiller edmundmiller deleted the STAR branch July 17, 2024 16:49
@edmundmiller edmundmiller mentioned this pull request Aug 5, 2024
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@edmundmiller @maxulysse