├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ └── feature_request.yml └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── assets ├── multiqc_config.yml ├── samplesheet.csv └── schema_input.json ├── conf ├── base.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config └── test_full.config ├── docs ├── images │ ├── tower_ce_enable_dragen.png │ ├── tower_pipeline_secrets.png │ ├── tower_secrets_dragen_password.png │ └── tower_secrets_dragen_username.png └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── dragen.nf │ └── dragen_buildhashtable.nf └── nf-core │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ └── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ ├── nextflow.config │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── subworkflows ├── local │ └── utils_nfcore_dragen_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 │ │ └── tags.yml │ ├── 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 │ │ └── tags.yml │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests └── data │ └── samplesheets │ └── samplesheet_test_illumina_amplicon.csv ├── tower.yml └── workflows └── dragen.nf /.editorconfig: 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