├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── CODEOWNERS ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md ├── actions │ ├── get-shards │ │ └── action.yml │ └── nf-test │ │ └── action.yml └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix_linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ ├── nf-test.yml │ ├── release-announcements.yml │ └── template-version-comment.yml ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── .vscode └── settings.json ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── email_template.html ├── email_template.txt ├── methods_description_template.yml ├── multiqc_config.yml ├── netmhc_software_meta.json ├── nf-core-epitopeprediction_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt ├── slackreport.json └── supported_alleles.json ├── bin ├── epaa.py ├── fasta2peptides.py ├── split_peptides.py ├── split_vcf_by_variants.py └── summarize_results.py ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config ├── test_fasta_output.config ├── test_full.config ├── test_grch38.config ├── test_mhcflurry.config ├── test_mhcnuggets.config ├── test_netmhciipan.config ├── test_netmhcpan.config ├── test_peptides.config ├── test_proteins.config └── test_wide_format_output.config ├── docs ├── README.md ├── images │ ├── nf-core-epitopeprediction_logo_dark.png │ └── nf-core-epitopeprediction_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── epytope_variant_prediction │ │ ├── environment.yml │ │ └── main.nf │ ├── fasta2peptides │ │ ├── environment.yml │ │ └── main.nf │ ├── merge_predictions │ │ ├── environment.yml │ │ ├── main.nf │ │ └── templates │ │ │ └── merge_predictions.py │ ├── mhcflurry │ │ ├── environment.yml │ │ └── main.nf │ ├── mhcnuggets │ │ ├── environment.yml │ │ ├── main.nf │ │ └── templates │ │ │ └── mhcnuggets.py │ ├── netmhciipan │ │ ├── environment.yml │ │ └── main.nf │ ├── netmhcpan │ │ ├── environment.yml │ │ └── main.nf │ ├── prepare_prediction_input │ │ ├── environment.yml │ │ ├── main.nf │ │ └── templates │ │ │ └── prepare_prediction_input.py │ ├── split_peptides │ │ ├── environment.yml │ │ └── main.nf │ ├── summarize_results │ │ ├── environment.yml │ │ └── main.nf │ ├── unpack_netmhc_software │ │ ├── environment.yml │ │ └── main.nf │ └── variant_split │ │ ├── environment.yml │ │ └── main.nf └── nf-core │ ├── bcftools │ └── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── cat │ └── cat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow_unzipped_zipped.config │ │ └── nextflow_zipped_unzipped.config │ ├── gunzip │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ └── snpsift │ └── split │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ └── main.nf.test.snap ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ ├── mhc_binding_prediction │ │ └── main.nf │ └── utils_nfcore_epitopeprediction_pipeline │ │ └── main.nf └── nf-core │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ └── nextflow.config │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ └── nextflow.config │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests ├── .nftignore ├── default.nf.test ├── default.nf.test.snap ├── fasta_output.nf.test ├── fasta_output.nf.test.snap ├── grch38.nf.test ├── grch38.nf.test.snap ├── mhcflurry.nf.test ├── mhcflurry.nf.test.snap ├── mhcnuggets.nf.test ├── mhcnuggets.nf.test.snap ├── nextflow.config ├── peptides.nf.test ├── peptides.nf.test.snap ├── proteins.nf.test ├── proteins.nf.test.snap ├── wide_format_output.nf.test └── wide_format_output.nf.test.snap ├── tower.yml └── workflows └── epitopeprediction.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 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