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port gatk4/createsequencedictionary to nf-test #5615

Merged
merged 13 commits into from
May 16, 2024
Merged

port gatk4/createsequencedictionary to nf-test #5615

merged 13 commits into from
May 16, 2024

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famosab
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@famosab famosab commented May 16, 2024

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 #3937

@famosab famosab requested review from maxulysse, ramprasadn and a team as code owners May 16, 2024 07:52
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famosab commented May 16, 2024

@maxulysse Seems to work with the CI, I am not checking the md5sum of the created dict.

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famosab commented May 16, 2024

For some reason now more nf-tests are triggered like summarizedexperiment...

@famosab famosab requested a review from maxulysse May 16, 2024 11:38
@maxulysse maxulysse enabled auto-merge May 16, 2024 11:43
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For some reason now more nf-tests are triggered like summarizedexperiment...

There must have been a merge at some point, but I see you fixed that with a master merge.
Well done

@maxulysse maxulysse disabled auto-merge May 16, 2024 11:48
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Oh sorry, I changed the tests with my commit 🤦

@maxulysse maxulysse added this pull request to the merge queue May 16, 2024
Merged via the queue into nf-core:master with commit e6fe277 May 16, 2024
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@famosab famosab deleted the gatk4-createseqdict branch May 16, 2024 12:24
tstoeriko pushed a commit to tstoeriko/nf-core-modules that referenced this pull request May 22, 2024
@famosab @maxulysse @tstoeriko
port gatk4/createsequencedictionary to nf-test (nf-core#5615)
a2e7d7e 
* port to nf-test

* update snap

* update tests to include versions

* port to nf-test

* update snap

* update tests to include versions

* change snapshot to read the dict

* check file md5sum

* Apply suggestions from code review

* update snap

---------

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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@maxulysse maxulysse maxulysse approved these changes

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

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