Update container image to include RTGtools

[Jorisvansteenbrugge]

PR checklist

Closes #6637

The container image assigned to happy/happy did not include RTG tools which is sometimes necessary. I updated the container image to a working version.

• [x] This comment contains a description of changes (with reason).

• [ ] Use BioConda and BioContainers if possible to fulfil software requirements.

  • I build a seqera wave container, but I'm not sure if that is desirable. Reviewer, please let me know if not.

[adamrtalbot]

Although RTG tools is recommended, it's not necessary.

Note, you can change the existing container using configuration:

process {
    withName: HAPPY_HAPPY {
        container = 'community.wave.seqera.io/library/hap.py_rtg-tools:2ebb433f3ce976d3'
    }
}

[Jorisvansteenbrugge]

Although RTG tools is recommended, it's not necessary.

Note, you can change the existing container using configuration:

process {
    withName: HAPPY_HAPPY {
        container = 'community.wave.seqera.io/library/hap.py_rtg-tools:2ebb433f3ce976d3'
    }
}

@adamrtalbot Thank you for your suggestion. I am aware that it is possible to configure the process to run with a different container image. However, as mentioned in issue #6637 it is currently not possible to use the vcfeval engine in hap.py with this module. Out of curiosity, wouldn't it make sense to provide a more complete container image by default?

[nvnieuwk]

Is vcfeval still not working with the seqera container?

[adamrtalbot]

@adamrtalbot Thank you for your suggestion. I am aware that it is possible to configure the process to run with a different container image. However, as mentioned in issue #6637 it is currently not possible to use the vcfeval engine in hap.py with this module. Out of curiosity, wouldn't it make sense to provide a more complete container image by default?

If you swap the container, you can enable vcfeval by adding the arguments, e.g. ext.args = '--engine=vcfeval'.

Images should be as small as possible for efficiency and portability. By including rtgeval we introduce complexity that will cause issues for a user.

Furthermore:

• the environment.yml isn't updated
• no input for the rtgtools cache is provided

Update the tool to fully work with rtgeval and add a test and we will have a fully working example.

[famosab]

@Jorisvansteenbrugge Do you still plan to finalize this? Or is the PR obsolete by now? :)

[Jorisvansteenbrugge]

@famosab Hi, sorry this PR went completely of my radar! I think it is is obsolete, my previous issues all seem to be solvable with user configuration so I will close it. Thank you for reminding me :)