Enable Spark for GATK

[maxulysse]

• 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]

cf nf-core/tools#336

[apeltzer]

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

[maxulysse]

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

[apeltzer]

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]

⚠️ Do not merge until HaplotypeCaller test is fixed.