LICENSE
README.md
pyproject.toml
setup.py
depictio/api/__init__.py
depictio/api/cache.py
depictio/api/celery_app.py
depictio/api/celery_worker.py
depictio/api/gunicorn_conf.py
depictio/api/logging_config.py
depictio/api/main.py
depictio/api/run.py
depictio/api/v1/__init__.py
depictio/api/v1/backup_strategy_manager.py
depictio/api/v1/celery_dispatch.py
depictio/api/v1/celery_tasks.py
depictio/api/v1/crypto.py
depictio/api/v1/db.py
depictio/api/v1/db_init.py
depictio/api/v1/db_init_reference_datasets.py
depictio/api/v1/deltatables_utils.py
depictio/api/v1/filter_links.py
depictio/api/v1/initialization.py
depictio/api/v1/json_response.py
depictio/api/v1/key_utils.py
depictio/api/v1/key_utils_base.py
depictio/api/v1/s3.py
depictio/api/v1/source_links.py
depictio/api/v1/utils.py
depictio/api/v1/configs/__init__.py
depictio/api/v1/configs/config.py
depictio/api/v1/configs/custom_logging.py
depictio/api/v1/configs/logging_init.py
depictio/api/v1/configs/security_headers.py
depictio/api/v1/configs/settings_models.py
depictio/catalog/__init__.py
depictio/catalog/catalog.schema.json
depictio/catalog/module.schema.json
depictio/catalog/output.schema.json
depictio/catalog/payload.py
depictio/catalog/happy/module.yaml
depictio/catalog/happy/roc.py
depictio/catalog/happy/roc.yaml
depictio/catalog/happy/summary.py
depictio/catalog/happy/summary.yaml
depictio/catalog/ivar/module.yaml
depictio/catalog/ivar/oncoplot_matrix.yaml
depictio/catalog/ivar/variants_long.py
depictio/catalog/ivar/variants_long.yaml
depictio/catalog/metaphlan/module.yaml
depictio/catalog/metaphlan/profile.yaml
depictio/catalog/mosdepth/amplicon_coverage.yaml
depictio/catalog/mosdepth/amplicon_heatmap.yaml
depictio/catalog/mosdepth/complex_heatmap_canonical.py
depictio/catalog/mosdepth/coverage_track_canonical.py
depictio/catalog/mosdepth/genome_coverage.yaml
depictio/catalog/mosdepth/module.yaml
depictio/catalog/multiqc/bcftools.yaml
depictio/catalog/multiqc/bowtie2.yaml
depictio/catalog/multiqc/cutadapt.yaml
depictio/catalog/multiqc/fastp.yaml
depictio/catalog/multiqc/fastqc.yaml
depictio/catalog/multiqc/happy.yaml
depictio/catalog/multiqc/ivar.yaml
depictio/catalog/multiqc/kraken.yaml
depictio/catalog/multiqc/module.yaml
depictio/catalog/multiqc/mosdepth.yaml
depictio/catalog/multiqc/quast.yaml
depictio/catalog/multiqc/samtools.yaml
depictio/catalog/multiqc/snpeff.yaml
depictio/catalog/multiqc/sompy.yaml
depictio/catalog/multiqc/summary.yaml
depictio/catalog/multiqc/summary_metrics.py
depictio/catalog/multiqc/summary_metrics.yaml
depictio/catalog/multiqc/truvari.yaml
depictio/catalog/nextclade/module.yaml
depictio/catalog/nextclade/nextclade_results.py
depictio/catalog/nextclade/report.yaml
depictio/catalog/pangolin/module.yaml
depictio/catalog/pangolin/pangolin_lineages.py
depictio/catalog/pangolin/report.yaml
depictio/catalog/qiime2/alpha_diversity.yaml
depictio/catalog/qiime2/alpha_diversity_multi_canonical.py
depictio/catalog/qiime2/alpha_rarefaction.py
depictio/catalog/qiime2/alpha_rarefaction.yaml
depictio/catalog/qiime2/alpha_rarefaction_summary.py
depictio/catalog/qiime2/ancombc.py
depictio/catalog/qiime2/ancombc.yaml
depictio/catalog/qiime2/bray_curtis.yaml
depictio/catalog/qiime2/clustered_heatmap.yaml
depictio/catalog/qiime2/embedding_pcoa.py
depictio/catalog/qiime2/embedding_pcoa.yaml
depictio/catalog/qiime2/ma.yaml
depictio/catalog/qiime2/module.yaml
depictio/catalog/qiime2/rarefaction_canonical.py
depictio/catalog/qiime2/rarefaction_canonical.yaml
depictio/catalog/qiime2/rel_abundance.yaml
depictio/catalog/qiime2/stacked_taxonomy_canonical.py
depictio/catalog/qiime2/stacked_taxonomy_canonical.yaml
depictio/catalog/qiime2/sunburst_canonical.yaml
depictio/catalog/qiime2/taxa_barplot.yaml
depictio/catalog/qiime2/taxonomy_composition.py
depictio/catalog/qiime2/taxonomy_composition.yaml
depictio/catalog/qiime2/taxonomy_heatmap.py
depictio/catalog/qiime2/taxonomy_heatmap.yaml
depictio/catalog/qiime2/tree_metadata.yaml
depictio/catalog/rtgtools/module.yaml
depictio/catalog/rtgtools/vcfeval_summary.py
depictio/catalog/rtgtools/vcfeval_summary.yaml
depictio/catalog/sompy/module.yaml
depictio/catalog/sompy/regions.py
depictio/catalog/sompy/regions.yaml
depictio/catalog/sompy/summary.py
depictio/catalog/sompy/summary.yaml
depictio/catalog/svanalyzer/module.yaml
depictio/catalog/svanalyzer/svbenchmark.py
depictio/catalog/svanalyzer/svbenchmark.yaml
depictio/catalog/truvari/module.yaml
depictio/catalog/truvari/summary.py
depictio/catalog/truvari/summary.yaml
depictio/catalog/wittyer/module.yaml
depictio/catalog/wittyer/summary.py
depictio/catalog/wittyer/summary.yaml
depictio/cli/__init__.py
depictio/cli/__main__.py
depictio/cli/cli_logging.py
depictio/cli/depictio_cli.py
depictio/cli/cli/__init__.py
depictio/cli/cli/commands/__init__.py
depictio/cli/cli/commands/backup.py
depictio/cli/cli/commands/catalog.py
depictio/cli/cli/commands/config.py
depictio/cli/cli/commands/dashboard.py
depictio/cli/cli/commands/data.py
depictio/cli/cli/commands/dev.py
depictio/cli/cli/commands/images.py
depictio/cli/cli/commands/migrate.py
depictio/cli/cli/commands/recipe.py
depictio/cli/cli/commands/run.py
depictio/cli/cli/commands/standalone.py
depictio/cli/cli/utils/__init__.py
depictio/cli/cli/utils/api_calls.py
depictio/cli/cli/utils/backup_validation.py
depictio/cli/cli/utils/common.py
depictio/cli/cli/utils/config.py
depictio/cli/cli/utils/deltatables.py
depictio/cli/cli/utils/file_utils.py
depictio/cli/cli/utils/helpers.py
depictio/cli/cli/utils/ingest_timing.py
depictio/cli/cli/utils/joins.py
depictio/cli/cli/utils/links.py
depictio/cli/cli/utils/mantine_templates.py
depictio/cli/cli/utils/multiqc_figures.py
depictio/cli/cli/utils/multiqc_processor.py
depictio/cli/cli/utils/process.py
depictio/cli/cli/utils/rich_utils.py
depictio/cli/cli/utils/sample_mapping.py
depictio/cli/cli/utils/scan.py
depictio/cli/cli/utils/scan_utils.py
depictio/cli/cli/utils/telemetry.py
depictio/cli/cli/utils/templates.py
depictio/cli/configs/nextflow/depictio.config
depictio/cli/configs/nextflow/example/README.md
depictio/cli/configs/nextflow/example/depictio_all_options.config
depictio/cli/configs/nextflow/example/depictio_dashboard.yaml
depictio/cli/configs/nextflow/example/depictio_project.yaml
depictio/cli/configs/nextflow/example/main.nf
depictio/cli/configs/nextflow/example/nextflow.config
depictio/models/__init__.py
depictio/models/config.py
depictio/models/logging.py
depictio/models/s3_utils.py
depictio/models/timestamps.py
depictio/models/utils.py
depictio/models/models/__init__.py
depictio/models/models/analytics.py
depictio/models/models/api.py
depictio/models/models/base.py
depictio/models/models/branding.py
depictio/models/models/cli.py
depictio/models/models/dashboards.py
depictio/models/models/data_collections.py
depictio/models/models/deltatables.py
depictio/models/models/files.py
depictio/models/models/google_oauth.py
depictio/models/models/jbrowse.py
depictio/models/models/joins.py
depictio/models/models/links.py
depictio/models/models/monitoring.py
depictio/models/models/multiqc_prerender.py
depictio/models/models/multiqc_reports.py
depictio/models/models/nextflow.py
depictio/models/models/projects.py
depictio/models/models/realtime.py
depictio/models/models/run_info.py
depictio/models/models/s3.py
depictio/models/models/snakemake.py
depictio/models/models/templates.py
depictio/models/models/transforms.py
depictio/models/models/users.py
depictio/models/models/workflows.py
depictio/models/models/data_collections_types/__init__.py
depictio/models/models/data_collections_types/geojson.py
depictio/models/models/data_collections_types/image.py
depictio/models/models/data_collections_types/jbrowse.py
depictio/models/models/data_collections_types/multiqc.py
depictio/models/models/data_collections_types/phylogeny.py
depictio/models/models/data_collections_types/table.py
depictio/models/models/data_collections_types/table_coordinates.py
depictio/projects/__init__.py
depictio/projects/init/advanced_viz_showcase/dashboards/ancombc.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/benchmark_ci.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/benchmark_confusion.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/benchmark_pr.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/benchmark_roc.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/categorical_flow.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/clustering_live.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/clustering_pca.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/clustering_pcoa.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/clustering_tsne.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/clustering_umap.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/complex_heatmap.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/coverage_track.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/da_barplot.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/dotplot.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/enrichment.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/lollipop.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/ma.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/manhattan.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/oncoplot.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/phylogeny.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/qq.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/rarefaction.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/stacked_taxonomy.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/sunburst.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/upset.yaml
depictio/projects/init/advanced_viz_showcase/dashboards/volcano.yaml
depictio/projects/init/catalog_conformance/template.yaml
depictio/projects/init/catalog_conformance/dashboards/overview.yaml
depictio/projects/init/iris/dashboards/overview.yaml
depictio/projects/init/iris/dashboards/petal_analysis.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/complex_heatmap.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/coverage_track.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/da_barplot.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/embedding.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/ma.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/qq.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/rarefaction.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/stacked_taxonomy.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/sunburst.yaml
depictio/projects/init/nfcore_megatests_showcase/dashboards/volcano.yaml
depictio/projects/init/penguins/dashboards/island_season.yaml
depictio/projects/init/penguins/dashboards/species_analysis.yaml
depictio/projects/nf-core/ampliseq/2.14.0/template.yaml
depictio/projects/nf-core/ampliseq/2.14.0/dashboards/full_analysis.yaml
depictio/projects/nf-core/ampliseq/2.14.0/recipes/taxonomy_rel_abundance.py
depictio/projects/nf-core/ampliseq/2.16.0/template.yaml
depictio/projects/nf-core/ampliseq/2.16.0/dashboards/base.yaml
depictio/projects/nf-core/ampliseq/2.16.0/dashboards/reference_extended.yaml
depictio/projects/nf-core/ampliseq/2.18.0/template.yaml
depictio/projects/nf-core/ampliseq/2.18.0/dashboards/base.yaml
depictio/projects/nf-core/ampliseq/2.18.0/dashboards/reference_extended.yaml
depictio/projects/nf-core/ampliseq/recipes/alpha_diversity.py
depictio/projects/nf-core/ampliseq/recipes/bray_curtis_canonical.py
depictio/projects/nf-core/ampliseq/recipes/complex_heatmap_canonical.py
depictio/projects/nf-core/ampliseq/recipes/ma_canonical.py
depictio/projects/nf-core/ampliseq/recipes/sankey_canonical.py
depictio/projects/nf-core/ampliseq/recipes/sidle_reconstructed.py
depictio/projects/nf-core/ampliseq/recipes/sidle_reconstruction_qc.py
depictio/projects/nf-core/ampliseq/recipes/sintax_rel_abundance.py
depictio/projects/nf-core/ampliseq/recipes/sunburst_canonical.py
depictio/projects/nf-core/ampliseq/recipes/taxonomy_rel_abundance.py
depictio/projects/nf-core/ampliseq/recipes/tree_metadata_canonical.py
depictio/projects/nf-core/ampliseq/recipes/upset_canonical.py
depictio/projects/nf-core/variantbenchmarking/1.4.0/template.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/indel/template.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/indel/dashboards/base.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/small/template.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/small/dashboards/base.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/structural/template.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/categories/structural/dashboards/base.yaml
depictio/projects/nf-core/variantbenchmarking/1.4.0/dashboards/base.yaml
depictio/projects/nf-core/viralrecon/3.0.0/template.yaml
depictio/projects/nf-core/viralrecon/3.0.0/dashboards/base.yaml
depictio/projects/nf-core/viralrecon/recipes/oncoplot_canonical.py
depictio/projects/nf-core/viralrecon/recipes/sankey_canonical.py
depictio/projects/nf-core/viralrecon/recipes/upset_canonical.py
depictio/projects/nf-core/viralrecon/recipes/variant_feature_matrix_canonical.py
depictio/projects/test/catalog_cli_smoke/dashboards/overview.yaml
depictio/projects/test/floating_map_demo/dashboards/two_tabs.yaml
depictio/projects/test/image_demo/dashboards/gallery.yaml
depictio/recipes/__init__.py
depictio/recipes/lib/__init__.py
depictio/recipes/lib/dimreduction.py
depictio/recipes/lib/lineage.py
depictio/telemetry/__init__.py
depictio/telemetry/buckets.py
depictio/telemetry/constants.py
depictio/telemetry/env.py
depictio/telemetry/gates.py
depictio/telemetry/k8s_resources.py
depictio/telemetry/posthog.py
depictio/telemetry/schema.py
depictio/telemetry/state.py
depictio_cli.egg-info/PKG-INFO
depictio_cli.egg-info/SOURCES.txt
depictio_cli.egg-info/dependency_links.txt
depictio_cli.egg-info/entry_points.txt
depictio_cli.egg-info/requires.txt
depictio_cli.egg-info/top_level.txt