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@anoronh4 anoronh4 commented Mar 26, 2025

PR checklist

Closes rnafusion#628

The reason I am only doing stub tests only is for practicality. The smallest reference i could get was about half a Gb, even when starting with the minigenome.fa and minigenome.gtf suggested by the tool's maintainers. I also considered adding starfusion/build so that i wouldn't have to store the reference on test-datasets, however this takes almost an hour to run on my system.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@anoronh4 anoronh4 marked this pull request as draft March 26, 2025 20:59
@anoronh4 anoronh4 changed the title add ctatsplicing/prepgenomelib add ctatsplicing/prepgenomelib and ctatsplicing/startocancerintrons Mar 31, 2025
@anoronh4 anoronh4 marked this pull request as ready for review April 3, 2025 21:43
@anoronh4 anoronh4 requested a review from atrigila April 4, 2025 17:22
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Great job on migrating these modules to nf-core modules! Left a few suggestions for small details. I am also tagging the author of these local modules, @nvnieuwk , so that he can give a final look in case I am missing something. There is an open PR here: #8107 which is adding the STARFUSION process, which could come very useful to add the non-stub test.

@delfiterradas delfiterradas self-assigned this Jul 31, 2025
@delfiterradas delfiterradas requested a review from nvnieuwk July 31, 2025 14:05
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This LGTM

@delfiterradas delfiterradas enabled auto-merge July 31, 2025 14:17
@delfiterradas delfiterradas added this pull request to the merge queue Jul 31, 2025
Merged via the queue into nf-core:master with commit 8476d6a Jul 31, 2025
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Migrate local CTATSPLICING_STARTOCANCERINTRONS to nf-core/modules

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