gatk/markduplicatesspark: add bam index output

[matthdsm]

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:
  • 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

[nvnieuwk]

LGTM, can it not create .crai files?

[matthdsm]

LGTM, can it not create .crai files?

Nope, only bai

[FriederikeHanssen]

There is a weird thing where crai end on bai iirc that messed up a bunch of stuff for me

[matthdsm]

There is a weird thing where crai end on bai iirc that messed up a bunch of stuff for me

AFAIK there's no support for cram indexes?

[FriederikeHanssen]

I was thinking of this issue: broadinstitute/gatk#5299 but anyways your point stands, it was just an add on

[matthdsm]

So this is good to go in your opinion?

[FriederikeHanssen]

yes, it is already approved, no?

[matthdsm]

Yeah, but Maxime asked us to refrain from approving each others PR's 😅