bump gatk4 version across the board

[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

[matthdsm]

needs fixin'

• [x] applybqsr (invald input)
• [x] applybsqrspark (invald input)
• [x] calculatecontamination
• [x] createsomaticpanelofnormals
• [x] filtermutectcalls
• [x] genomicsdbimport
• [x] getpileupsummaries A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "genome.interval_list" is not valid for this input.
• [x] haplotypecaller
• [x] learnreadorientationmodel
• [x] markduplicates (wrong reference fasta)
• [x] markduplicatesspark

           A USER ERROR has occurred: Fasta dict file for reference genome.fasta does not exist. Please see                                                                                                  
         http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.     

• [x] mutect2
• [x] printsvevidence
• [x] splitncigerreads

[matthdsm]

@nf-core/core, the CI tests keep failing due to GHA being unable to fetch one file or another from the test-data repo. I'm having the same issues when testing locally.

I did however, check if all inputs are present in the tests (yes) and IMO everything should work. Do I keep fiddling with the CI until I get it to work? Or should I go ahead and merge?

[SPPearce]

@nf-core/core, the CI tests keep failing due to GHA being unable to fetch one file or another from the test-data repo. I'm having the same issues when testing locally.

I did however, check if all inputs are present in the tests (yes) and IMO everything should work. Do I keep fiddling with the CI until I get it to work? Or should I go ahead and merge?

Some of the checks are generating output files but have different md5sums (applybqsr, applybqsrspark, markduplicates, markduplicatesspark, splitncigarreads). HaptolypeCaller seems odd too, giving AssertionError: versions.yml not found in the output directory. : https://github.com/nf-core/modules/actions/runs/3271044686/jobs/5384544244

[matthdsm]

I've no idea, why this happens... I'm regenerating the checksum but get no differences

[matthdsm]

CI still failing because of subworkflows

• [ ] gatk_tumor_normal_somatic_variant_calling
• [ ] gatk_create_som_pon
• [ ] gatk_tumor_only_somatic_variant_calling

[matthdsm]

The offending subworkflows seem to be legacy cases with a bunch of wrong inputs. I've no experience with the tools, so I don't intend to try and fix them here. These should be attended to in another PR IMO.

Opinions?

[FriederikeHanssen]

applybqsrsoark has a mismatched checksum, why can that not be fixed?

[matthdsm]

ughh.... I already fixed that checksum a couple of times 😞 Seems to be different each time it goes through the CI. Singularity and conda pass...

[FriederikeHanssen]

https://github.com/nf-core/modules/pull/1965#discussion_r999479089 all the version.yml are removed, from here I gather this may not be intentional. might be worth to wait until this is cleared up

[matthdsm]

Yep, wanted only to remove the checksum. My regex was ... not so good.

[matthdsm]

Tests pass where they need to, checksums seem to be ok this time around. versions.yml were re-added.

Good to merge? (Please say yes)

[maxulysse]

@matthdsm Can you list the failed subworkflows in an issue, so we know which one we need to update?

[matthdsm]

@matthdsm Can you list the failed subworkflows in an issue, so we know which one we need to update?

Done!