├── .editorconfig ├── .gitbook.yaml ├── .github ├── CODEOWNERS ├── PULL_REQUEST_TEMPLATE.md ├── actions │ └── nf-test-action │ │ └── action.yml ├── conda_skip.yml ├── generate_codeowners.sh ├── manual_CODEOWNERS ├── release │ ├── RELEASE.md │ ├── draft_releases.png │ ├── publish.png │ ├── release_pr.png │ ├── releases.png │ └── repo.png ├── skip_nf_test.json └── workflows │ ├── assign_codeowners.yml │ ├── gitbook-sync.yml │ ├── nf-test.yml │ ├── pytest-workflow.yml │ ├── skipped-nf-test.yml │ └── update_summary.py ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc ├── .prettierrc.yml ├── LICENSE ├── README.md ├── modules ├── environment-schema.json ├── meta-schema.json ├── msk │ ├── .gitkeep │ ├── custom │ │ └── splitfastqbylane │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ └── usr │ │ │ │ └── bin │ │ │ │ └── split_lanes_awk.sh │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── facets │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── gatk4 │ │ └── applybqsr │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── gbcms │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── genomenexus │ │ ├── annotationpipeline │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ └── vcf2maf │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── genotypevariants │ │ └── all │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── mutect1 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── nextflow.config │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── neoantigenediting │ │ ├── aligntoiedb │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── align_neoantigens_to_IEDB.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ └── computefitness │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ └── usr │ │ │ │ └── bin │ │ │ │ ├── EpitopeDistance.py │ │ │ │ ├── compute_fitness.py │ │ │ │ └── distance_data │ │ │ │ └── epitope_distance_model_parameters.json │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── neoantigenutils │ │ ├── convertannotjson │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── convertannotjson.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── formatnetmhcpan │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── format_netmhcpan_output.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── generatehlastring │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── generateHLAString.sh │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── generatemutfasta │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── generateMutFasta.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ └── neoantigeninput │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ └── usr │ │ │ │ └── bin │ │ │ │ └── generate_input.py │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── neosv │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── netmhc3 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── resources │ │ │ └── usr │ │ │ │ └── bin │ │ │ │ └── trim_hla.py │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── netmhcpan4 │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── netmhcstabpan │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── phylowgs │ │ ├── createinput │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── create_phylowgs_inputs.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ ├── multievolve │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ ├── parsecnvs │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ ├── resources │ │ │ │ └── usr │ │ │ │ │ └── bin │ │ │ │ │ └── parse_cnvs.py │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── writeresults │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── polysolver │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ ├── ppflagfixer │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── pvmaf │ │ ├── concat │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ ├── nextflow.config │ │ │ │ └── tags.yml │ │ └── tagtraceback │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── rediscoverte │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── salmon │ │ ├── index │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ │ ├── main.nf.test │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── tags.yml │ │ └── quant │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── tags.yml │ └── snppileup │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.config │ │ └── tags.yml └── yaml-schema.json ├── nf-test.config ├── subworkflows ├── msk │ ├── genome_nexus │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── tags.yml │ ├── neoantigen_editing │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ ├── netmhcstabandpan │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── tags.yml │ 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