Clair3

[robert-a-forsyth]

PR checklist

Closes #XXX
Adds Clair3 module for germline small variant calling

• 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

[robert-a-forsyth]

I need to upload test data to the nf-core test data repository, it's unclear to me if I should add it in this pull request. The website says to contact the nf-core modules slack channel, which I will do now. I have removed all TODO statements, except the one telling myself to change the path of the test data to the location of the newly uploaded test data

[SPPearce]

I need to upload test data to the nf-core test data repository, it's unclear to me if I should add it in this pull request. The website says to contact the nf-core modules slack channel, which I will do now. I have removed all TODO statements, except the one telling myself to change the path of the test data to the location of the newly uploaded test data

The data lives in the modules branch of the test-datasets repo, so would definitely need to be a separate PR.

[robert-a-forsyth]

I need to upload test data to the nf-core test data repository, it's unclear to me if I should add it in this pull request. The website says to contact the nf-core modules slack channel, which I will do now. I have removed all TODO statements, except the one telling myself to change the path of the test data to the location of the newly uploaded test data

The data lives in the modules branch of the test-datasets repo, so would definitely need to be a separate PR.

Opened a pull request just now at (nf-core/test-datasets#1520). I'll remove the comments when that one is approved and change the test set to its location