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add more stubs gatk4 #6673

Merged
merged 5 commits into from
Sep 25, 2024
Merged

add more stubs gatk4 #6673

merged 5 commits into from
Sep 25, 2024

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famosab
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@famosab famosab commented Sep 20, 2024 •
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PR checklist

Closes #XXX

  • 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

Relates to #4570

nvnieuwk
nvnieuwk approved these changes Sep 23, 2024
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@nvnieuwk nvnieuwk left a comment

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LGTM!!

modules/nf-core/gatk4/fastqtosam/tests/main.nf.test Outdated Show resolved Hide resolved
@famosab famosab added this pull request to the merge queue Sep 25, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Sep 25, 2024
@famosab famosab added this pull request to the merge queue Sep 25, 2024
Merged via the queue into nf-core:master with commit 679f45c Sep 25, 2024
20 checks passed
@famosab famosab deleted the gatk-stub2 branch September 25, 2024 08:21
herpov pushed a commit to herpov/modules that referenced this pull request Oct 2, 2024
@famosab
add more stubs gatk4 (nf-core#6673)
025747b 
* add stubs

* run lint --fix

* fix formatting
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@nvnieuwk nvnieuwk nvnieuwk approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

@ntoda03 ntoda03 Awaiting requested review from ntoda03

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2 participants
@famosab @nvnieuwk