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New Subworkflow: Bam_trim_primers_ivar #3130

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wants to merge 10 commits into from
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New Subworkflow: Bam_trim_primers_ivar #3130

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Joon-Klaps
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@Joon-Klaps Joon-Klaps commented Mar 27, 2023 •
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PR checklist

Addresses first bullet from nf-core/viralrecon#371

adds the subworkflow bam_trim_primers_ivar used in nf-core/viralrecon to nf-core/modules

  • 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
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • 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

@Joon-Klaps Joon-Klaps self-assigned this Mar 27, 2023
@Joon-Klaps Joon-Klaps marked this pull request as draft March 27, 2023 13:26
@Joon-Klaps Joon-Klaps added the hackathon2023 Topic for the hackathon of March 2023 label Mar 27, 2023
@Joon-Klaps Joon-Klaps requested a review from nvnieuwk March 27, 2023 13:52
@Joon-Klaps Joon-Klaps marked this pull request as ready for review March 27, 2023 13:53
nvnieuwk
nvnieuwk previously requested changes Mar 27, 2023
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@Joon-Klaps Joon-Klaps requested a review from nvnieuwk March 27, 2023 15:38
@Joon-Klaps Joon-Klaps changed the title Bam trim primers ivar New Subworkflow: Bam_trim_primers_ivar Mar 27, 2023
nvnieuwk
nvnieuwk reviewed Mar 28, 2023
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@nvnieuwk nvnieuwk left a comment

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One more small comment and then you are good to go!

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@Joon-Klaps
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Not Sure why conda test is failing though..

@nvnieuwk
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It seems to be something tool specific. Maybe a wrong conda package?

@Joon-Klaps
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It seems to be something tool specific. Maybe a wrong conda package?

Yeah... doesn't seem something I'll be able to finish as part of this PR... andersen-lab/ivar#93

@edmundmiller edmundmiller requested a review from a team as a code owner October 19, 2023 16:26
@sateeshperi sateeshperi added the mismatched hashes Conda/singularity hashes aren't right label Dec 25, 2023
@Joon-Klaps Joon-Klaps closed this Jun 3, 2024
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@nvnieuwk nvnieuwk nvnieuwk left review comments

@sateeshperi sateeshperi Awaiting requested review from sateeshperi sateeshperi was automatically assigned from nf-core/nf-test

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@Joon-Klaps Joon-Klaps

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@Joon-Klaps @nvnieuwk @SPPearce @sateeshperi @maxulysse