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Enable Spark for GATK #76

Merged
merged 12 commits into from
Dec 18, 2019
Merged

Enable Spark for GATK #76

merged 12 commits into from
Dec 18, 2019

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maxulysse
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  • Add GATK Spark possibilities to Sarek
  • Now use gatk4-spark instead of gatk4
  • Remove runOptions = "-u \$(id -u):\$(id -g)" in nextflow.config to enable Spark possibilities
  • Close Use spark for GATK #64

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 necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: guidelines

@maxulysse maxulysse added the enhancement New feature or request label Dec 10, 2019
@maxulysse maxulysse self-assigned this Dec 10, 2019
@maxulysse maxulysse requested review from apeltzer and a team December 10, 2019 14:26
@maxulysse
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cf nf-core/tools#336

@apeltzer
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Maybe we could add a comment to the template that pipelines using SPARK shouldn't have these options set?

@maxulysse
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No idea about that one is this runOptions = "-u \$(id -u):\$(id -g)" really that important?

@apeltzer
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We had some discussions whether we need it at all or should have it by default. Even in the nextflow issue tracker it's not been clear whether this should be a default setting in general for nextflows docker integration ...?

@maxulysse
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⚠️ Do not merge until HaplotypeCaller test is fixed.

@maxulysse maxulysse merged commit a7ee2d6 into nf-core:dev Dec 18, 2019
@maxulysse maxulysse deleted the GATKBESTPRACTICES branch December 18, 2019 09:27
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2 participants