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Update container image to include RTGtools #6639
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Although RTG tools is recommended, it's not necessary. Note, you can change the existing container using configuration:
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@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? |
Is vcfeval still not working with the seqera container? |
If you swap the container, you can enable vcfeval by adding the arguments, e.g. 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:
Update the tool to fully work with rtgeval and add a test and we will have a fully working example. |
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.
This comment contains a description of changes (with reason).
Use BioConda and BioContainers if possible to fulfil software requirements.