├── .devcontainer ├── devcontainer.json └── setup.sh ├── .gitattributes ├── .github ├── .dockstore.yml ├── 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 ├── nf-core-molkart_logo_light.png ├── samplesheet.csv ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── apply_clahe.dask.py ├── collect_QC.py ├── create_anndata.py ├── crop_hdf5.py ├── crop_tiff.py ├── maskfilter.py ├── spot2cell.py └── stack.py ├── conf ├── base.config ├── modules.config ├── test.config └── test_full.config ├── docs ├── README.md ├── images │ ├── molkart_workflow.png │ ├── nf-core-molkart_logo_dark.png │ └── nf-core-molkart_logo_light.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── clahe │ │ └── main.nf │ ├── createanndata │ │ └── main.nf │ ├── createstack │ │ └── main.nf │ ├── crophdf5 │ │ └── main.nf │ ├── croptiff │ │ └── main.nf │ ├── maskfilter │ │ └── main.nf │ ├── molkartqc │ │ └── main.nf │ ├── molkartqcpng │ │ └── main.nf │ ├── spot2cell │ │ └── main.nf │ └── tiffh5convert │ │ └── main.nf └── nf-core │ ├── cellpose │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow_wflows.config │ │ └── tags.yml │ ├── deepcell │ └── mesmer │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── ilastik │ ├── multicut │ │ ├── main.nf │ │ └── meta.yml │ └── pixelclassification │ │ ├── main.nf │ │ └── meta.yml │ ├── mindagap │ ├── duplicatefinder │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── mindagap │ │ ├── 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 │ └── stardist │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── main.nf.test.snap │ └── nextflow.config ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── ro-crate-metadata.json ├── subworkflows ├── local │ └── utils_nfcore_molkart_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 ├── main.nf.test ├── main.nf.test.snap ├── nextflow.config └── tags.yml ├── tower.yml └── workflows └── molkart.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 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