[robert-a-forsyth]

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 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:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

Adds ClairS, small somatic variant caller for tumor-normal paired samples. Unfortunately Conda isn't available for this, but it does have support on singularity and docker

[SPPearce]

Is it possible for the tool to be added to bioconda?
That would also make biocontainers docker and singularity images automatically.
We don't really like having custom docker images.

[famosab]

@robert-a-forsyth any news on this? do you have time to tackle it? :)

[SPPearce]

@robert-a-forsyth , do you have time to finish this off?

[DylanMHouse]

Hi, is there any updates on this module?

[DylanMHouse]

I will ask the developers of ClairS if it would be possible to add the bioconda package, and maybe we could finalise this module? I am actually needing this so it would be great to have it on nf-core

[SPPearce]

@DylanMHouse , feel free to take over the implementation.
You can make your own bioconda recipe (relatively straightforward these days with LLMs)

[DylanMHouse]

@SPPearce I 'll continue development of this module then. I will wait a bit until the developers respond to my issue for a few days. Otherwise, I'll make that biocoda recipe and adapt the module to it.