caddforge-docs 0.3.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- caddforge_docs/__init__.py +1 -0
- caddforge_docs/cli.py +20 -0
- caddforge_docs/server.py +124 -0
- caddforge_docs/site/404.html +2118 -0
- caddforge_docs/site/assets/_mkdocstrings.css +237 -0
- caddforge_docs/site/assets/images/favicon.png +0 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js +16 -0
- caddforge_docs/site/assets/javascripts/bundle.d7400e89.min.js.map +7 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js +42 -0
- caddforge_docs/site/assets/javascripts/workers/search.2c215733.min.js.map +7 -0
- caddforge_docs/site/assets/licenses/W3C-Software-and-Document-2015.txt +15 -0
- caddforge_docs/site/assets/licenses/autogrid-COPYING-GPL-2.txt +339 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-COPYING-GPL-3.txt +674 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-EXCEPTION.txt +73 -0
- caddforge_docs/site/assets/licenses/autogrid-GCC-RUNTIME-NOTICE.txt +24 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-COPYING.txt +674 -0
- caddforge_docs/site/assets/licenses/caddforge-opencosmors-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/caddforge-unidock-tools-LICENSE.txt +202 -0
- caddforge_docs/site/assets/licenses/clipboard-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/escape-html-LICENSE.txt +2 -0
- caddforge_docs/site/assets/licenses/focus-visible-LICENSE.txt +4 -0
- caddforge_docs/site/assets/licenses/fontawesome-LICENSE.txt +165 -0
- caddforge_docs/site/assets/licenses/fuzzaldrin-plus-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/lunr-LICENSE.txt +17 -0
- caddforge_docs/site/assets/licenses/material-LICENSE.txt +20 -0
- caddforge_docs/site/assets/licenses/material-design-color-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/material-shadows-LICENSE.txt +31 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/mkdocs-material-extensions-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocs-section-index-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/mkdocstrings-python-LICENSE.txt +15 -0
- caddforge_docs/site/assets/licenses/octicons-LICENSE.txt +21 -0
- caddforge_docs/site/assets/licenses/preact-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/properdocs-LICENSE.txt +26 -0
- caddforge_docs/site/assets/licenses/pymdown-extensions-LICENSE.txt +113 -0
- caddforge_docs/site/assets/licenses/rxjs-LICENSE.txt +180 -0
- caddforge_docs/site/assets/licenses/simple-LICENSE.txt +30 -0
- caddforge_docs/site/assets/licenses/tiny-emitter-LICENSE.txt +19 -0
- caddforge_docs/site/assets/licenses/tslib-LICENSE.txt +12 -0
- caddforge_docs/site/assets/licenses/zeno-rocha-components-LICENSE.txt +22 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/main.ec1eaa64.min.css.map +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css +1 -0
- caddforge_docs/site/assets/stylesheets/palette.ab4e12ef.min.css.map +1 -0
- caddforge_docs/site/core/cli/index.html +2446 -0
- caddforge_docs/site/core/concepts/index.html +2340 -0
- caddforge_docs/site/core/configuration/index.html +2300 -0
- caddforge_docs/site/core/index.html +2170 -0
- caddforge_docs/site/core/jobs-results/index.html +2315 -0
- caddforge_docs/site/core/plugins/index.html +2200 -0
- caddforge_docs/site/core/slurm/index.html +2562 -0
- caddforge_docs/site/development/ci-publishing/index.html +2345 -0
- caddforge_docs/site/development/contributing/index.html +2311 -0
- caddforge_docs/site/development/documentation/index.html +2380 -0
- caddforge_docs/site/development/index.html +2201 -0
- caddforge_docs/site/development/release-notes/index.html +2504 -0
- caddforge_docs/site/development/release-readiness/index.html +2333 -0
- caddforge_docs/site/development/security/index.html +2181 -0
- caddforge_docs/site/development/tool-authoring/index.html +2435 -0
- caddforge_docs/site/examples/index.html +2465 -0
- caddforge_docs/site/examples/manifest.json +158 -0
- caddforge_docs/site/examples/minimize/component_overrides.yaml +14 -0
- caddforge_docs/site/examples/minimize/ligand_only.yaml +13 -0
- caddforge_docs/site/examples/minimize/pipeline_docking.yaml +84 -0
- caddforge_docs/site/examples/minimize/pipeline_scatter.yaml +49 -0
- caddforge_docs/site/examples/minimize/pocket_free_shell_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/pocket_restrained.yaml +13 -0
- caddforge_docs/site/examples/minimize/prepared_metal.yaml +14 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_fixed.yaml +13 -0
- caddforge_docs/site/examples/minimize/sidechains_free_backbone_restrained.yaml +13 -0
- caddforge_docs/site/examples/pipelines/descriptor-model-and-candidate-filter.yaml +44 -0
- caddforge_docs/site/examples/pipelines/dock-extract-and-minimize-poses.yaml +85 -0
- caddforge_docs/site/examples/pipelines/docking-screen-and-rescore.yaml +55 -0
- caddforge_docs/site/examples/pipelines/flexible-gnina-to-openbpmd-to-md-to-abfe.yaml +189 -0
- caddforge_docs/site/examples/pipelines/gnina-flexible-complex-artifacts.yaml +52 -0
- caddforge_docs/site/examples/pipelines/minimize-a-multi-pose-sdf.yaml +46 -0
- caddforge_docs/site/examples/pipelines/pose-level-md-selection.yaml +95 -0
- caddforge_docs/site/examples/pipelines/result-collection-and-diagnostics.yaml +55 -0
- caddforge_docs/site/examples/quickstart/diagnostics.yaml +8 -0
- caddforge_docs/site/examples/quickstart/index.html +2172 -0
- caddforge_docs/site/examples/quickstart/pipeline.yaml +23 -0
- caddforge_docs/site/examples/quickstart/run.py +18 -0
- caddforge_docs/site/examples/quickstart/run_pipeline.py +6 -0
- caddforge_docs/site/examples/quickstart/scores.csv +7 -0
- caddforge_docs/site/examples/quickstart/values.csv +31 -0
- caddforge_docs/site/examples/run_tool.py +40 -0
- caddforge_docs/site/examples/tools/datascience-csv-scatter.yaml +17 -0
- caddforge_docs/site/examples/tools/datascience-distribution-diagnostics.yaml +10 -0
- caddforge_docs/site/examples/tools/descriptors-ani-conformers.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-ani-psa.yaml +9 -0
- caddforge_docs/site/examples/tools/descriptors-cluster-molecules.yaml +11 -0
- caddforge_docs/site/examples/tools/descriptors-phesa.yaml +7 -0
- caddforge_docs/site/examples/tools/docking-gnina.yaml +12 -0
- caddforge_docs/site/examples/tools/docking-idockya.yaml +8 -0
- caddforge_docs/site/examples/tools/docking-unidock.yaml +12 -0
- caddforge_docs/site/examples/tools/fep-openfe-abfe.yaml +53 -0
- caddforge_docs/site/examples/tools/fep-openfe-rbfe-septop.yaml +23 -0
- caddforge_docs/site/examples/tools/md-center-and-align.yaml +16 -0
- caddforge_docs/site/examples/tools/md-cluster-representative.yaml +16 -0
- caddforge_docs/site/examples/tools/md-extract-frames.yaml +17 -0
- caddforge_docs/site/examples/tools/md-fix-structure.yaml +20 -0
- caddforge_docs/site/examples/tools/md-grand.yaml +28 -0
- caddforge_docs/site/examples/tools/md-inducia.yaml +29 -0
- caddforge_docs/site/examples/tools/md-minimize.yaml +13 -0
- caddforge_docs/site/examples/tools/md-openbpmd.yaml +11 -0
- caddforge_docs/site/examples/tools/md-plain-md.yaml +28 -0
- caddforge_docs/site/examples/tools/ml-explore-classifier.yaml +5 -0
- caddforge_docs/site/examples/tools/ml-model-factory.yaml +32 -0
- caddforge_docs/site/examples/tools/ml-model-zoo.yaml +16 -0
- caddforge_docs/site/examples/tools/ml-pca.yaml +10 -0
- caddforge_docs/site/examples/tools/ml-simple-gp.yaml +17 -0
- caddforge_docs/site/examples/tools/qm-transfer-free-energy.yaml +11 -0
- caddforge_docs/site/explanation/references/index.html +2218 -0
- caddforge_docs/site/explanation/reproducibility/index.html +2306 -0
- caddforge_docs/site/explanation/third-party-notices/index.html +2599 -0
- caddforge_docs/site/getting-started/first-pipeline/index.html +2195 -0
- caddforge_docs/site/getting-started/first-workflow/index.html +2329 -0
- caddforge_docs/site/getting-started/index.html +2200 -0
- caddforge_docs/site/getting-started/installation/index.html +2541 -0
- caddforge_docs/site/gui/index.html +2267 -0
- caddforge_docs/site/gui/plugin-authoring/index.html +2280 -0
- caddforge_docs/site/gui/walkthrough/index.html +2181 -0
- caddforge_docs/site/how-to/jobs/index.html +2195 -0
- caddforge_docs/site/how-to/scatter/index.html +2193 -0
- caddforge_docs/site/how-to/troubleshooting/index.html +2429 -0
- caddforge_docs/site/index.html +2359 -0
- caddforge_docs/site/objects.inv +0 -0
- caddforge_docs/site/pipelines/artifacts/index.html +2314 -0
- caddforge_docs/site/pipelines/built-ins/index.html +2670 -0
- caddforge_docs/site/pipelines/examples/index.html +3186 -0
- caddforge_docs/site/pipelines/index.html +2164 -0
- caddforge_docs/site/pipelines/specification/index.html +2278 -0
- caddforge_docs/site/plugins/datascience/index.html +2405 -0
- caddforge_docs/site/plugins/descriptors/index.html +2609 -0
- caddforge_docs/site/plugins/docking/index.html +2480 -0
- caddforge_docs/site/plugins/fep/index.html +2508 -0
- caddforge_docs/site/plugins/index.html +2216 -0
- caddforge_docs/site/plugins/md/index.html +3795 -0
- caddforge_docs/site/plugins/ml/index.html +2815 -0
- caddforge_docs/site/plugins/qm/index.html +2309 -0
- caddforge_docs/site/plugins/version-matrix/index.html +2449 -0
- caddforge_docs/site/reference/api/index.html +4414 -0
- caddforge_docs/site/reference/index.html +2166 -0
- caddforge_docs/site/search/search_index.json +1 -0
- caddforge_docs/site/sitemap.xml +191 -0
- caddforge_docs/site/sitemap.xml.gz +0 -0
- caddforge_docs-0.3.0.dist-info/METADATA +158 -0
- caddforge_docs-0.3.0.dist-info/RECORD +152 -0
- caddforge_docs-0.3.0.dist-info/WHEEL +4 -0
- caddforge_docs-0.3.0.dist-info/entry_points.txt +2 -0
- caddforge_docs-0.3.0.dist-info/licenses/LICENSE +21 -0
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
|
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|
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469
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470
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<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="">
|
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<span class="md-ellipsis">
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477
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How-to Guides
|
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<span class="md-nav__icon md-icon"></span>
|
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</label>
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487
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488
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
|
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489
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<label class="md-nav__title" for="__nav_3">
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<span class="md-nav__icon md-icon"></span>
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How-to Guides
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495
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</label>
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<ul class="md-nav__list" data-md-scrollfix>
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<li class="md-nav__item">
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<a href="../../how-to/jobs/" class="md-nav__link">
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<span class="md-ellipsis">
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Jobs and Results
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</a>
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<li class="md-nav__item">
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<a href="../../how-to/scatter/" class="md-nav__link">
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537
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<span class="md-ellipsis">
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540
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541
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Scatter and Reduce
|
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542
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543
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545
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</a>
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<li class="md-nav__item">
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562
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<a href="../../how-to/troubleshooting/" class="md-nav__link">
|
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563
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564
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565
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566
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<span class="md-ellipsis">
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567
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|
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568
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|
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569
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Troubleshooting
|
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570
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|
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571
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|
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</span>
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</a>
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581
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582
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|
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</ul>
|
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584
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</nav>
|
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585
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586
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</li>
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<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
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621
|
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|
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622
|
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|
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623
|
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|
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624
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<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
|
|
625
|
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|
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626
|
+
|
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627
|
+
<div class="md-nav__link md-nav__container">
|
|
628
|
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<a href="../../core/" class="md-nav__link ">
|
|
629
|
+
|
|
630
|
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|
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631
|
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|
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632
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<span class="md-ellipsis">
|
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633
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|
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634
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|
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635
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Core
|
|
636
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|
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637
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|
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638
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|
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639
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</span>
|
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640
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|
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641
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|
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642
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|
|
643
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</a>
|
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644
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|
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645
|
+
|
|
646
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+
<label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
|
|
647
|
+
<span class="md-nav__icon md-icon"></span>
|
|
648
|
+
</label>
|
|
649
|
+
|
|
650
|
+
</div>
|
|
651
|
+
|
|
652
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
|
|
653
|
+
<label class="md-nav__title" for="__nav_4">
|
|
654
|
+
<span class="md-nav__icon md-icon"></span>
|
|
655
|
+
|
|
656
|
+
|
|
657
|
+
Core
|
|
658
|
+
|
|
659
|
+
|
|
660
|
+
</label>
|
|
661
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
662
|
+
|
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663
|
+
|
|
664
|
+
|
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665
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|
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666
|
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|
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667
|
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|
|
668
|
+
|
|
669
|
+
<li class="md-nav__item">
|
|
670
|
+
<a href="../../core/concepts/" class="md-nav__link">
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
<span class="md-ellipsis">
|
|
675
|
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|
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676
|
+
|
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677
|
+
Concepts
|
|
678
|
+
|
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679
|
+
|
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680
|
+
|
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681
|
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</span>
|
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682
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|
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684
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|
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685
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</a>
|
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686
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</li>
|
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|
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696
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|
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697
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<li class="md-nav__item">
|
|
698
|
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<a href="../../core/configuration/" class="md-nav__link">
|
|
699
|
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|
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700
|
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|
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701
|
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|
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702
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<span class="md-ellipsis">
|
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703
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|
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704
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|
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705
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Configuration
|
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706
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|
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707
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|
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708
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|
|
709
|
+
</span>
|
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710
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|
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711
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|
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712
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|
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713
|
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</a>
|
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714
|
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|
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715
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716
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719
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720
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|
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721
|
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|
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722
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|
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723
|
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|
|
724
|
+
|
|
725
|
+
<li class="md-nav__item">
|
|
726
|
+
<a href="../../core/cli/" class="md-nav__link">
|
|
727
|
+
|
|
728
|
+
|
|
729
|
+
|
|
730
|
+
<span class="md-ellipsis">
|
|
731
|
+
|
|
732
|
+
|
|
733
|
+
CLI
|
|
734
|
+
|
|
735
|
+
|
|
736
|
+
|
|
737
|
+
</span>
|
|
738
|
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|
|
739
|
+
|
|
740
|
+
|
|
741
|
+
</a>
|
|
742
|
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</li>
|
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743
|
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|
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744
|
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|
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745
|
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|
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746
|
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747
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748
|
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749
|
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|
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750
|
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|
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751
|
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|
|
752
|
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|
|
753
|
+
<li class="md-nav__item">
|
|
754
|
+
<a href="../../core/jobs-results/" class="md-nav__link">
|
|
755
|
+
|
|
756
|
+
|
|
757
|
+
|
|
758
|
+
<span class="md-ellipsis">
|
|
759
|
+
|
|
760
|
+
|
|
761
|
+
Jobs and Results
|
|
762
|
+
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
</span>
|
|
766
|
+
|
|
767
|
+
|
|
768
|
+
|
|
769
|
+
</a>
|
|
770
|
+
</li>
|
|
771
|
+
|
|
772
|
+
|
|
773
|
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|
|
774
|
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|
|
775
|
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|
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776
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|
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777
|
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|
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778
|
+
|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
<li class="md-nav__item">
|
|
782
|
+
<a href="../../core/slurm/" class="md-nav__link">
|
|
783
|
+
|
|
784
|
+
|
|
785
|
+
|
|
786
|
+
<span class="md-ellipsis">
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
Slurm Backend
|
|
790
|
+
|
|
791
|
+
|
|
792
|
+
|
|
793
|
+
</span>
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
|
|
797
|
+
</a>
|
|
798
|
+
</li>
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
|
|
806
|
+
|
|
807
|
+
|
|
808
|
+
|
|
809
|
+
<li class="md-nav__item">
|
|
810
|
+
<a href="../../core/plugins/" class="md-nav__link">
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
<span class="md-ellipsis">
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
Plugins
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
|
|
821
|
+
</span>
|
|
822
|
+
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
</a>
|
|
826
|
+
</li>
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
</ul>
|
|
832
|
+
</nav>
|
|
833
|
+
|
|
834
|
+
</li>
|
|
835
|
+
|
|
836
|
+
|
|
837
|
+
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
|
|
851
|
+
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
|
|
858
|
+
|
|
859
|
+
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
|
|
864
|
+
|
|
865
|
+
|
|
866
|
+
<li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
|
|
867
|
+
|
|
868
|
+
|
|
869
|
+
|
|
870
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
<div class="md-nav__link md-nav__container">
|
|
874
|
+
<a href="../" class="md-nav__link ">
|
|
875
|
+
|
|
876
|
+
|
|
877
|
+
|
|
878
|
+
<span class="md-ellipsis">
|
|
879
|
+
|
|
880
|
+
|
|
881
|
+
Pipelines
|
|
882
|
+
|
|
883
|
+
|
|
884
|
+
|
|
885
|
+
</span>
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
|
|
889
|
+
</a>
|
|
890
|
+
|
|
891
|
+
|
|
892
|
+
<label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
|
|
893
|
+
<span class="md-nav__icon md-icon"></span>
|
|
894
|
+
</label>
|
|
895
|
+
|
|
896
|
+
</div>
|
|
897
|
+
|
|
898
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
|
|
899
|
+
<label class="md-nav__title" for="__nav_5">
|
|
900
|
+
<span class="md-nav__icon md-icon"></span>
|
|
901
|
+
|
|
902
|
+
|
|
903
|
+
Pipelines
|
|
904
|
+
|
|
905
|
+
|
|
906
|
+
</label>
|
|
907
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
908
|
+
|
|
909
|
+
|
|
910
|
+
|
|
911
|
+
|
|
912
|
+
|
|
913
|
+
|
|
914
|
+
|
|
915
|
+
<li class="md-nav__item">
|
|
916
|
+
<a href="../specification/" class="md-nav__link">
|
|
917
|
+
|
|
918
|
+
|
|
919
|
+
|
|
920
|
+
<span class="md-ellipsis">
|
|
921
|
+
|
|
922
|
+
|
|
923
|
+
Specification
|
|
924
|
+
|
|
925
|
+
|
|
926
|
+
|
|
927
|
+
</span>
|
|
928
|
+
|
|
929
|
+
|
|
930
|
+
|
|
931
|
+
</a>
|
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932
|
+
</li>
|
|
933
|
+
|
|
934
|
+
|
|
935
|
+
|
|
936
|
+
|
|
937
|
+
|
|
938
|
+
|
|
939
|
+
|
|
940
|
+
|
|
941
|
+
|
|
942
|
+
|
|
943
|
+
|
|
944
|
+
|
|
945
|
+
<li class="md-nav__item md-nav__item--active">
|
|
946
|
+
|
|
947
|
+
<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
|
|
948
|
+
|
|
949
|
+
|
|
950
|
+
|
|
951
|
+
|
|
952
|
+
|
|
953
|
+
<label class="md-nav__link md-nav__link--active" for="__toc">
|
|
954
|
+
|
|
955
|
+
|
|
956
|
+
|
|
957
|
+
<span class="md-ellipsis">
|
|
958
|
+
|
|
959
|
+
|
|
960
|
+
Artifacts
|
|
961
|
+
|
|
962
|
+
|
|
963
|
+
|
|
964
|
+
</span>
|
|
965
|
+
|
|
966
|
+
|
|
967
|
+
|
|
968
|
+
<span class="md-nav__icon md-icon"></span>
|
|
969
|
+
</label>
|
|
970
|
+
|
|
971
|
+
<a href="./" class="md-nav__link md-nav__link--active">
|
|
972
|
+
|
|
973
|
+
|
|
974
|
+
|
|
975
|
+
<span class="md-ellipsis">
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
Artifacts
|
|
979
|
+
|
|
980
|
+
|
|
981
|
+
|
|
982
|
+
</span>
|
|
983
|
+
|
|
984
|
+
|
|
985
|
+
|
|
986
|
+
</a>
|
|
987
|
+
|
|
988
|
+
|
|
989
|
+
|
|
990
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
991
|
+
|
|
992
|
+
|
|
993
|
+
|
|
994
|
+
|
|
995
|
+
|
|
996
|
+
|
|
997
|
+
<label class="md-nav__title" for="__toc">
|
|
998
|
+
<span class="md-nav__icon md-icon"></span>
|
|
999
|
+
Table of contents
|
|
1000
|
+
</label>
|
|
1001
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
1002
|
+
|
|
1003
|
+
<li class="md-nav__item">
|
|
1004
|
+
<a href="#input-and-output-ports" class="md-nav__link">
|
|
1005
|
+
<span class="md-ellipsis">
|
|
1006
|
+
|
|
1007
|
+
Input and output ports
|
|
1008
|
+
|
|
1009
|
+
</span>
|
|
1010
|
+
</a>
|
|
1011
|
+
|
|
1012
|
+
</li>
|
|
1013
|
+
|
|
1014
|
+
<li class="md-nav__item">
|
|
1015
|
+
<a href="#scatter-provenance" class="md-nav__link">
|
|
1016
|
+
<span class="md-ellipsis">
|
|
1017
|
+
|
|
1018
|
+
Scatter provenance
|
|
1019
|
+
|
|
1020
|
+
</span>
|
|
1021
|
+
</a>
|
|
1022
|
+
|
|
1023
|
+
</li>
|
|
1024
|
+
|
|
1025
|
+
<li class="md-nav__item">
|
|
1026
|
+
<a href="#compressed-boundaries" class="md-nav__link">
|
|
1027
|
+
<span class="md-ellipsis">
|
|
1028
|
+
|
|
1029
|
+
Compressed boundaries
|
|
1030
|
+
|
|
1031
|
+
</span>
|
|
1032
|
+
</a>
|
|
1033
|
+
|
|
1034
|
+
</li>
|
|
1035
|
+
|
|
1036
|
+
</ul>
|
|
1037
|
+
|
|
1038
|
+
</nav>
|
|
1039
|
+
|
|
1040
|
+
</li>
|
|
1041
|
+
|
|
1042
|
+
|
|
1043
|
+
|
|
1044
|
+
|
|
1045
|
+
|
|
1046
|
+
|
|
1047
|
+
|
|
1048
|
+
|
|
1049
|
+
|
|
1050
|
+
|
|
1051
|
+
<li class="md-nav__item">
|
|
1052
|
+
<a href="../built-ins/" class="md-nav__link">
|
|
1053
|
+
|
|
1054
|
+
|
|
1055
|
+
|
|
1056
|
+
<span class="md-ellipsis">
|
|
1057
|
+
|
|
1058
|
+
|
|
1059
|
+
Built-in Stages
|
|
1060
|
+
|
|
1061
|
+
|
|
1062
|
+
|
|
1063
|
+
</span>
|
|
1064
|
+
|
|
1065
|
+
|
|
1066
|
+
|
|
1067
|
+
</a>
|
|
1068
|
+
</li>
|
|
1069
|
+
|
|
1070
|
+
|
|
1071
|
+
|
|
1072
|
+
|
|
1073
|
+
|
|
1074
|
+
|
|
1075
|
+
|
|
1076
|
+
|
|
1077
|
+
|
|
1078
|
+
|
|
1079
|
+
<li class="md-nav__item">
|
|
1080
|
+
<a href="../examples/" class="md-nav__link">
|
|
1081
|
+
|
|
1082
|
+
|
|
1083
|
+
|
|
1084
|
+
<span class="md-ellipsis">
|
|
1085
|
+
|
|
1086
|
+
|
|
1087
|
+
Examples
|
|
1088
|
+
|
|
1089
|
+
|
|
1090
|
+
|
|
1091
|
+
</span>
|
|
1092
|
+
|
|
1093
|
+
|
|
1094
|
+
|
|
1095
|
+
</a>
|
|
1096
|
+
</li>
|
|
1097
|
+
|
|
1098
|
+
|
|
1099
|
+
|
|
1100
|
+
|
|
1101
|
+
</ul>
|
|
1102
|
+
</nav>
|
|
1103
|
+
|
|
1104
|
+
</li>
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
|
|
1108
|
+
|
|
1109
|
+
|
|
1110
|
+
|
|
1111
|
+
|
|
1112
|
+
|
|
1113
|
+
|
|
1114
|
+
|
|
1115
|
+
|
|
1116
|
+
|
|
1117
|
+
|
|
1118
|
+
|
|
1119
|
+
|
|
1120
|
+
|
|
1121
|
+
|
|
1122
|
+
|
|
1123
|
+
|
|
1124
|
+
|
|
1125
|
+
|
|
1126
|
+
|
|
1127
|
+
|
|
1128
|
+
|
|
1129
|
+
|
|
1130
|
+
|
|
1131
|
+
|
|
1132
|
+
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
|
|
1136
|
+
|
|
1137
|
+
|
|
1138
|
+
|
|
1139
|
+
|
|
1140
|
+
|
|
1141
|
+
|
|
1142
|
+
<li class="md-nav__item md-nav__item--section md-nav__item--nested">
|
|
1143
|
+
|
|
1144
|
+
|
|
1145
|
+
|
|
1146
|
+
<input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
|
|
1147
|
+
|
|
1148
|
+
|
|
1149
|
+
<div class="md-nav__link md-nav__container">
|
|
1150
|
+
<a href="../../plugins/" class="md-nav__link ">
|
|
1151
|
+
|
|
1152
|
+
|
|
1153
|
+
|
|
1154
|
+
<span class="md-ellipsis">
|
|
1155
|
+
|
|
1156
|
+
|
|
1157
|
+
Plugins
|
|
1158
|
+
|
|
1159
|
+
|
|
1160
|
+
|
|
1161
|
+
</span>
|
|
1162
|
+
|
|
1163
|
+
|
|
1164
|
+
|
|
1165
|
+
</a>
|
|
1166
|
+
|
|
1167
|
+
|
|
1168
|
+
<label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
|
|
1169
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1170
|
+
</label>
|
|
1171
|
+
|
|
1172
|
+
</div>
|
|
1173
|
+
|
|
1174
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
|
|
1175
|
+
<label class="md-nav__title" for="__nav_6">
|
|
1176
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1177
|
+
|
|
1178
|
+
|
|
1179
|
+
Plugins
|
|
1180
|
+
|
|
1181
|
+
|
|
1182
|
+
</label>
|
|
1183
|
+
<ul class="md-nav__list" data-md-scrollfix>
|
|
1184
|
+
|
|
1185
|
+
|
|
1186
|
+
|
|
1187
|
+
|
|
1188
|
+
|
|
1189
|
+
|
|
1190
|
+
|
|
1191
|
+
<li class="md-nav__item">
|
|
1192
|
+
<a href="../../plugins/version-matrix/" class="md-nav__link">
|
|
1193
|
+
|
|
1194
|
+
|
|
1195
|
+
|
|
1196
|
+
<span class="md-ellipsis">
|
|
1197
|
+
|
|
1198
|
+
|
|
1199
|
+
Version Matrix
|
|
1200
|
+
|
|
1201
|
+
|
|
1202
|
+
|
|
1203
|
+
</span>
|
|
1204
|
+
|
|
1205
|
+
|
|
1206
|
+
|
|
1207
|
+
</a>
|
|
1208
|
+
</li>
|
|
1209
|
+
|
|
1210
|
+
|
|
1211
|
+
|
|
1212
|
+
|
|
1213
|
+
|
|
1214
|
+
|
|
1215
|
+
|
|
1216
|
+
|
|
1217
|
+
|
|
1218
|
+
|
|
1219
|
+
<li class="md-nav__item">
|
|
1220
|
+
<a href="../../plugins/docking/" class="md-nav__link">
|
|
1221
|
+
|
|
1222
|
+
|
|
1223
|
+
|
|
1224
|
+
<span class="md-ellipsis">
|
|
1225
|
+
|
|
1226
|
+
|
|
1227
|
+
Docking
|
|
1228
|
+
|
|
1229
|
+
|
|
1230
|
+
|
|
1231
|
+
</span>
|
|
1232
|
+
|
|
1233
|
+
|
|
1234
|
+
|
|
1235
|
+
</a>
|
|
1236
|
+
</li>
|
|
1237
|
+
|
|
1238
|
+
|
|
1239
|
+
|
|
1240
|
+
|
|
1241
|
+
|
|
1242
|
+
|
|
1243
|
+
|
|
1244
|
+
|
|
1245
|
+
|
|
1246
|
+
|
|
1247
|
+
<li class="md-nav__item">
|
|
1248
|
+
<a href="../../plugins/descriptors/" class="md-nav__link">
|
|
1249
|
+
|
|
1250
|
+
|
|
1251
|
+
|
|
1252
|
+
<span class="md-ellipsis">
|
|
1253
|
+
|
|
1254
|
+
|
|
1255
|
+
Descriptors
|
|
1256
|
+
|
|
1257
|
+
|
|
1258
|
+
|
|
1259
|
+
</span>
|
|
1260
|
+
|
|
1261
|
+
|
|
1262
|
+
|
|
1263
|
+
</a>
|
|
1264
|
+
</li>
|
|
1265
|
+
|
|
1266
|
+
|
|
1267
|
+
|
|
1268
|
+
|
|
1269
|
+
|
|
1270
|
+
|
|
1271
|
+
|
|
1272
|
+
|
|
1273
|
+
|
|
1274
|
+
|
|
1275
|
+
<li class="md-nav__item">
|
|
1276
|
+
<a href="../../plugins/md/" class="md-nav__link">
|
|
1277
|
+
|
|
1278
|
+
|
|
1279
|
+
|
|
1280
|
+
<span class="md-ellipsis">
|
|
1281
|
+
|
|
1282
|
+
|
|
1283
|
+
MD
|
|
1284
|
+
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
</span>
|
|
1288
|
+
|
|
1289
|
+
|
|
1290
|
+
|
|
1291
|
+
</a>
|
|
1292
|
+
</li>
|
|
1293
|
+
|
|
1294
|
+
|
|
1295
|
+
|
|
1296
|
+
|
|
1297
|
+
|
|
1298
|
+
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
|
|
1302
|
+
|
|
1303
|
+
<li class="md-nav__item">
|
|
1304
|
+
<a href="../../plugins/fep/" class="md-nav__link">
|
|
1305
|
+
|
|
1306
|
+
|
|
1307
|
+
|
|
1308
|
+
<span class="md-ellipsis">
|
|
1309
|
+
|
|
1310
|
+
|
|
1311
|
+
FEP
|
|
1312
|
+
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
</span>
|
|
1316
|
+
|
|
1317
|
+
|
|
1318
|
+
|
|
1319
|
+
</a>
|
|
1320
|
+
</li>
|
|
1321
|
+
|
|
1322
|
+
|
|
1323
|
+
|
|
1324
|
+
|
|
1325
|
+
|
|
1326
|
+
|
|
1327
|
+
|
|
1328
|
+
|
|
1329
|
+
|
|
1330
|
+
|
|
1331
|
+
<li class="md-nav__item">
|
|
1332
|
+
<a href="../../plugins/qm/" class="md-nav__link">
|
|
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Plugin GUI Authoring
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Public Python API
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Example Library
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Example Data Provenance
|
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|
|
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1732
|
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|
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|
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<label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="">
|
|
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|
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|
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<span class="md-ellipsis">
|
|
1738
|
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|
|
1739
|
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|
|
1740
|
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Explanation
|
|
1741
|
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|
|
1742
|
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|
|
1743
|
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|
|
1744
|
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</span>
|
|
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|
|
1747
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|
|
1748
|
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<span class="md-nav__icon md-icon"></span>
|
|
1749
|
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</label>
|
|
1750
|
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|
|
1751
|
+
<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false">
|
|
1752
|
+
<label class="md-nav__title" for="__nav_9">
|
|
1753
|
+
<span class="md-nav__icon md-icon"></span>
|
|
1754
|
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|
|
1755
|
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|
|
1756
|
+
Explanation
|
|
1757
|
+
|
|
1758
|
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|
|
1759
|
+
</label>
|
|
1760
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<ul class="md-nav__list" data-md-scrollfix>
|
|
1761
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|
|
1762
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|
|
1763
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1764
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Security Reporting
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|
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|
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Release Readiness
|
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2084
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2086
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2101
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|
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2103
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<a href="../../development/ci-publishing/" class="md-nav__link">
|
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2104
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2105
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|
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2106
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+
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2107
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+
<span class="md-ellipsis">
|
|
2108
|
+
|
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2109
|
+
|
|
2110
|
+
CI and Publishing
|
|
2111
|
+
|
|
2112
|
+
|
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2113
|
+
|
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2114
|
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</span>
|
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2115
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|
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2116
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2117
|
+
|
|
2118
|
+
</a>
|
|
2119
|
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|
|
2120
|
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|
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2121
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+
|
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2122
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+
|
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2123
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+
|
|
2124
|
+
</ul>
|
|
2125
|
+
</nav>
|
|
2126
|
+
|
|
2127
|
+
</li>
|
|
2128
|
+
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2129
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+
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2130
|
+
|
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2131
|
+
</ul>
|
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2132
|
+
</nav>
|
|
2133
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</div>
|
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2134
|
+
</div>
|
|
2135
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+
</div>
|
|
2136
|
+
|
|
2137
|
+
|
|
2138
|
+
|
|
2139
|
+
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
|
|
2140
|
+
<div class="md-sidebar__scrollwrap">
|
|
2141
|
+
<div class="md-sidebar__inner">
|
|
2142
|
+
|
|
2143
|
+
|
|
2144
|
+
<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
|
|
2145
|
+
|
|
2146
|
+
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|
2147
|
+
|
|
2148
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|
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2149
|
+
|
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2150
|
+
|
|
2151
|
+
<label class="md-nav__title" for="__toc">
|
|
2152
|
+
<span class="md-nav__icon md-icon"></span>
|
|
2153
|
+
Table of contents
|
|
2154
|
+
</label>
|
|
2155
|
+
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
|
|
2156
|
+
|
|
2157
|
+
<li class="md-nav__item">
|
|
2158
|
+
<a href="#input-and-output-ports" class="md-nav__link">
|
|
2159
|
+
<span class="md-ellipsis">
|
|
2160
|
+
|
|
2161
|
+
Input and output ports
|
|
2162
|
+
|
|
2163
|
+
</span>
|
|
2164
|
+
</a>
|
|
2165
|
+
|
|
2166
|
+
</li>
|
|
2167
|
+
|
|
2168
|
+
<li class="md-nav__item">
|
|
2169
|
+
<a href="#scatter-provenance" class="md-nav__link">
|
|
2170
|
+
<span class="md-ellipsis">
|
|
2171
|
+
|
|
2172
|
+
Scatter provenance
|
|
2173
|
+
|
|
2174
|
+
</span>
|
|
2175
|
+
</a>
|
|
2176
|
+
|
|
2177
|
+
</li>
|
|
2178
|
+
|
|
2179
|
+
<li class="md-nav__item">
|
|
2180
|
+
<a href="#compressed-boundaries" class="md-nav__link">
|
|
2181
|
+
<span class="md-ellipsis">
|
|
2182
|
+
|
|
2183
|
+
Compressed boundaries
|
|
2184
|
+
|
|
2185
|
+
</span>
|
|
2186
|
+
</a>
|
|
2187
|
+
|
|
2188
|
+
</li>
|
|
2189
|
+
|
|
2190
|
+
</ul>
|
|
2191
|
+
|
|
2192
|
+
</nav>
|
|
2193
|
+
</div>
|
|
2194
|
+
</div>
|
|
2195
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+
</div>
|
|
2196
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+
|
|
2197
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+
|
|
2198
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<h1 id="artifacts">Artifacts<a class="headerlink" href="#artifacts" title="Permanent link">¶</a></h1>
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<p>Pipeline stages exchange <code>ArtifactRef</code> objects. Downstream stages should not guess tool-specific
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directory layouts.</p>
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<p>Important fields:</p>
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<ul>
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<li><code>path</code>: primary path or manifest path</li>
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<li><code>paths</code>: multi-path collection, such as one SDF file per retained pose</li>
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<li><code>metadata</code>: provenance hints, result path keys, scatter manifests, and path-collection markers</li>
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</ul>
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<h2 id="input-and-output-ports">Input and output ports<a class="headerlink" href="#input-and-output-ports" title="Permanent link">¶</a></h2>
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<p>Tool plugins can expose pipeline contracts:</p>
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<ul>
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<li><code>InputPort(name, kind, config_field)</code> maps a pipeline input to a config field.</li>
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<li><code>OutputPort(name, kind, result_path_key)</code> maps a pipeline output to a key in <code>Result.paths</code>.</li>
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<li><code>OutputPort(..., required=False)</code> marks outputs that are produced only for some configurations.
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Missing optional result path keys are skipped instead of failing the stage.</li>
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<li><code>OutputPort(..., path_collection_column="pose_file")</code> treats the result path as a CSV manifest
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and exposes the named column as <code>ArtifactRef.paths</code>. The artifact <code>path</code> remains the manifest, so
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downstream stages can keep both provenance and exact file paths.</li>
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</ul>
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<h2 id="scatter-provenance">Scatter provenance<a class="headerlink" href="#scatter-provenance" title="Permanent link">¶</a></h2>
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<p>Scatter over file inputs supports SDF, CSV, line-based, and auto splitting. Scatter over path
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collections supports one job per path or chunked path lists depending on the downstream config field
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type.</p>
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<p>When a scattered tool stage receives multiple path-collection inputs and non-scatter inputs have the
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same number of paths as the scatter input, CADDForge binds those paths by row order for each shard.
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Use this for paired artifacts selected from the same manifest row, such as an ABFE ligand SDF plus
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its matching protein PDB. If the paired config field is typed as <code>list[Path]</code>, each shard receives a
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one-item list containing the matching path. Use this for tools such as plain MD where the complex PDB
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is a single <code>Path</code> but the matching ligand SDF is passed through a list field. The scatter field is
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still the only field listed under <code>scatter.by</code>.</p>
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<p>For path-collection scatter, the executor writes <code>scatter_manifest.csv</code> so downstream stages can
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join results back to ligand, pose, molecule, or source path metadata.</p>
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<p>When scattered CSV, TSV, SDF, JSONL, or manifest outputs are reduced to one canonical file,
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downstream stages bind that merged file and split it again according to their own scatter contract.
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The reduced artifact can still retain individual shard paths for provenance. Genuine path
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collections continue to bind their member paths directly.</p>
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<h2 id="compressed-boundaries">Compressed boundaries<a class="headerlink" href="#compressed-boundaries" title="Permanent link">¶</a></h2>
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<p>Pipeline tools can consume and produce <code>.csv.gz</code>, <code>.tsv.gz</code>, and <code>.sdf.gz</code> through explicit port
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contracts. Inputs stay compressed between stages and are materialized only at tool runtime. Core
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atomically compresses declared outputs after the tool succeeds and persists the finalized path in
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the canonical result. A scattered stage must use a unique compressed output destination per shard.</p>
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</article>
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