Add somatic to DSL2

[maxulysse]

nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

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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 necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: CONTRIBUTING.md

[FriederikeHanssen]

FYI: I think the BioContainers for bwa-mem2 have been updated. It is not shown yet on the website but they are listed on https://quay.io/repository/biocontainers/bwa-mem2?tab=tags and https://depot.galaxyproject.org/singularity/ . Mulled container is still missing though as far as I see: https://quay.io/repository/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40?tab=tags

[FriederikeHanssen]

FYI: I think the BioContainers for bwa-mem2 have been updated. It is not shown yet on the website but they are listed on https://quay.io/repository/biocontainers/bwa-mem2?tab=tags and https://depot.galaxyproject.org/singularity/ . Mulled container is still missing though as far as I see: https://quay.io/repository/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40?tab=tags

There is anew bwa-mem2 container now:

 conda (params.enable_conda ? "bioconda::bwa-mem2=2.1--he513fc3_0 bioconda::samtools=1.11--h6270b1f_0" : null)
    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0" 
    } else {
        container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0"
    }

[maxulysse]

FYI: I think the BioContainers for bwa-mem2 have been updated. It is not shown yet on the website but they are listed on https://quay.io/repository/biocontainers/bwa-mem2?tab=tags and https://depot.galaxyproject.org/singularity/ . Mulled container is still missing though as far as I see: https://quay.io/repository/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40?tab=tags

There is anew bwa-mem2 container now:

 conda (params.enable_conda ? "bioconda::bwa-mem2=2.1--he513fc3_0 bioconda::samtools=1.11--h6270b1f_0" : null)
    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0" 
    } else {
        container "quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:e6f0d20c9d78572ddbbf00d8767ee6ff865edd4e-0"
    }

I noticed that samtools is on version 1.11 now, I'll try and update the bwa mem container with the samtools 1.10