Code

Implement Neo subworkflow#8

Code

Merged

scwatts merged 23 commits intofeatures-block-one-previewnf-core/oncoanalyser:features-block-one-previewfrom neo-subworkflownf-core/oncoanalyser:neo-subworkflowCopy head branch name to clipboardMay 30, 2024

+686-5

Commits

Commits on May 29, 2024

• Frame out Neo subworkflow

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  9898841

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• First cut of Neoepitope subworkflow

  

  charlesshale

  authored and

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• Get stub runs working

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  e9a04b3

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• Clean up

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• Get local run working on sample data

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• Set Neo to run only when specified

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• Fix Neo stubs

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• Provide Neo cancer type from samplesheet

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• Fix Neo scorer RNA sample ID and VCF input

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• Minor fixes

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• Update to latest Neo 1.2_beta build artefact

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• Update Neo reference data paths

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• Move neo_prediction.nf subworkflow for consistency

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• Adjust Neo to fit with alignment subworkflow

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• Adjust indenting

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• Indent Neo subworkflow to match nf-core style

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• Use Bioconda for Neo annotate fusion process

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• Add environment file for annotate fusion process

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• Rename some Neo subworkflow variables for clarity

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• Add meta.yml for annotate fusion process

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• Add meta.yml for Neo finder process

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• Add meta.yml for Neo scorer process

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Commits on May 30, 2024

• Apply linting

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