toil.lib.integration¶
Contains functions for integrating Toil with external services such as Dockstore.
Attributes¶
Functions¶
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Returns True if a workflow string smells Dockstore-y. |
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Parse a Dockstore workflow URL or TSR ID to a string that is definitely a TRS ID. |
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Parse a TRS ID to workflow and optional version. |
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Given a Dockstore URL or TRS identifier, get the root WDL or CWL URL for the workflow. |
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Find the real workflow URL or filename from a command line argument. |
Module Contents¶
- toil.lib.integration.logger¶
- toil.lib.integration.is_dockstore_workflow(workflow)[source]¶
Returns True if a workflow string smells Dockstore-y.
Detects Dockstore page URLs and strings that could be Dockstore TRS IDs.
- toil.lib.integration.find_trs_spec(workflow)[source]¶
Parse a Dockstore workflow URL or TSR ID to a string that is definitely a TRS ID.
- toil.lib.integration.parse_trs_spec(trs_spec)[source]¶
Parse a TRS ID to workflow and optional version.
- toil.lib.integration.get_workflow_root_from_dockstore(workflow, supported_languages=None)[source]¶
Given a Dockstore URL or TRS identifier, get the root WDL or CWL URL for the workflow.
Accepts inputs like:
https://dockstore.org/workflows/github.com/dockstore-testing/md5sum-checker:master?tab=info
#workflow/github.com/dockstore-testing/md5sum-checker
Assumes the input is actually one of the supported formats. See is_dockstore_workflow().
TODO: Needs to handle multi-workflow files if Dockstore can.