├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── clean-up.yml │ ├── download_pipeline.yml │ ├── fix-linting.yml │ ├── linting.yml │ ├── linting_comment.yml │ └── release-announcements.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── 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 ├── nf-core-omicsgenetraitassociation_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin └── check_samplesheet.py ├── conf ├── base.config ├── cma_mea.config ├── igenomes.config ├── modules.config ├── test.config ├── test_full.config └── test_local.config ├── docs ├── README.md ├── images │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ ├── nf-core-omicgenetraitassociation_metro_map.png │ ├── nf-core-omicsgenetraitassociation_logo_dark.png │ └── nf-core-omicsgenetraitassociation_logo_light.png ├── output.md └── usage.md ├── lib ├── NfcoreTemplate.groovy ├── Utils.groovy ├── WorkflowMain.groovy └── WorkflowOmicsgenetraitassociation.groovy ├── main.nf ├── modules.json ├── modules ├── local │ ├── cma │ │ ├── cma │ │ │ └── main.nf │ │ └── format_cma_input │ │ │ ├── bin │ │ │ └── format_cma_input.py │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── mea │ │ ├── go_analysis │ │ │ ├── main.nf │ │ │ └── templates │ │ │ │ └── ORA_cmd.R │ │ ├── merge_ora_and_summary │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ └── templates │ │ │ │ └── mergeORAandSummary.py │ │ ├── pascal │ │ │ ├── main.nf │ │ │ └── templates │ │ │ │ └── runPascal.py │ │ ├── postprocess │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ └── templates │ │ │ │ └── processPascalOutput.py │ │ └── preprocess │ │ │ ├── environment.yml │ │ │ ├── main.nf │ │ │ └── templates │ │ │ └── preProcessForPascal.py │ ├── mmap │ │ ├── mmap │ │ │ └── main.nf │ │ └── mmap_parse │ │ │ ├── bin │ │ │ └── parse_MMAP_output.py │ │ │ ├── environment.yml │ │ │ └── main.nf │ ├── pascal │ │ ├── bin │ │ │ └── pascal.py │ │ └── main.nf │ └── samplesheet_check.nf └── nf-core │ ├── custom │ └── dumpsoftwareversions │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ ├── templates │ │ └── dumpsoftwareversions.py │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── tags.yml │ ├── 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 │ └── tags.yml ├── nextflow.config ├── nextflow_schema.json ├── pyproject.toml ├── subworkflows └── local │ ├── cma.nf │ ├── input_check.nf │ ├── mmap.nf │ └── pascal.nf ├── tower.yml └── workflows └── omicsgenetraitassociation.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/omicsgenetraitassociation/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/omicsgenetraitassociation/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 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