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Update fastq_align_star for nf-test and handle transcriptome alignment better #4927

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merged 10 commits into from
Feb 16, 2024

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@pinin4fjords pinin4fjords commented Feb 15, 2024

In this PR:

  • Update fastq_align_star for nf-test
  • Replace test data with RNA-seq data used by STAR module, that will actually align (test data used previously was not aligning).
  • Add analagous sorting, indexing etc for the transcriptome BAM that can be produced by STAR.
  • Supply a trancriptome fasta file that can be used by samtools stats

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 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@pinin4fjords pinin4fjords requested review from JoseEspinosa and a team as code owners February 15, 2024 16:46
@pinin4fjords pinin4fjords requested review from ahvigil and removed request for a team February 15, 2024 16:46
@pinin4fjords pinin4fjords marked this pull request as draft February 15, 2024 16:48
@pinin4fjords pinin4fjords marked this pull request as ready for review February 16, 2024 09:11
subworkflows/nf-core/fastq_align_star/main.nf Outdated Show resolved Hide resolved
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@mashehu mashehu left a comment

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sorry, the last review wasn't supposed to be an approval, but a request for comments

subworkflows/nf-core/fastq_align_star/meta.yml Outdated Show resolved Hide resolved
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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thanks @mashehu !

@pinin4fjords pinin4fjords added this pull request to the merge queue Feb 16, 2024
Merged via the queue into master with commit 0fa6ac0 Feb 16, 2024
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@pinin4fjords pinin4fjords deleted the improve_fastq_align_star branch February 16, 2024 11:41
jch-13 pushed a commit to jch-13/modules that referenced this pull request Mar 19, 2024
…t better (nf-core#4927)

* Update fastq_align_star for nf-test and handle transcriptome alignment better

* Remove backup file

* Replace test data with RNA-specific that will actually align

* Appease eclint

* Add extra test for when trancriptome bam produced but transcriptome not supplied

* Fix snapshots

* Remove convenience transcriptome creation

* Update subworkflows/nf-core/fastq_align_star/meta.yml

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

---------

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
…t better (nf-core#4927)

* Update fastq_align_star for nf-test and handle transcriptome alignment better

* Remove backup file

* Replace test data with RNA-specific that will actually align

* Appease eclint

* Add extra test for when trancriptome bam produced but transcriptome not supplied

* Fix snapshots

* Remove convenience transcriptome creation

* Update subworkflows/nf-core/fastq_align_star/meta.yml

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

---------

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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3 participants