Module/oncokb maf annotation - #189
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buehlere
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Aug 26, 2025
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Adding a oncokb maf annotation module. I created the oncokb folder so we can add other oncokb scripts to it in the future, such as annotate CNV, among others. You need to add a oncokb token for this to work. I tested it locally with mine. Also, the container PR is here mskcc-omics-workflows/containers#27 but the module doesn't currently use this container, it uses a placeholder on my own dockerhub.
feature/<module_name>for modules, orfeature/<subworkflow_name>for subworkflows. For modules, if there is a subcommand use:feature/<module_name>/<module_subcommand>.versions.ymlfile.label.nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile dockernf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularitynf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile condanf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile dockernf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularitynf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda