Language Support

Ideally, all features in Dockstore would be available in all languages. However, due to time constraints and gaps in our knowledge of different workflows, some features of Dockstore are not available in all languages.

To help lay out what parts of Dockstore are available in which languages, we cover the following guide for what features are available on the Dockstore site and in the Dockstore command-line utility.

Feature	CWL	WDL	Nextflow	Galaxy
Dockstore site
Tool registration	Yes	Yes	No	No
Workflow registration	Yes	Yes	Yes	Yes
Hosted Workflows	Yes	Yes	Yes	Yes
DAG Display	Yes (cwl version=>1.1) [1]	Yes (wdl version<=1.0)	Limited support	Limited support
Tool Tab Display	Yes (cwl version=>1.1)	Yes (wdl version<=1.0)	Yes	Limited support
Launch-with Platforms for workflows	BioData Catalyst [2] Cavatica [3] CGC [4]	AnVIL [5] BioData Catalyst [6] DNAnexus DNAstack [7] Terra [8]	Not yet!	Galaxy [9]
Metadata Display	Yes	Yes (wdl version<=1.0)	Yes	Yes
Dockstore CLI
Local workflow engines	cwltool, Cromwell	Cromwell [10]	Nextflow	None
File Provisioning In	Local File System HTTP FTP GCS via plugins S3 via plugins Data Object Service	Local File System HTTP FTP GCS via plugins S3 via plugins Data Object Service	Local File System HTTP FTP S3	No
Plugins Support	GCS s3 s3cmd icgc-get Data Object Service	GCS s3 s3cmd icgc-get Data Object Service	No	No
File Provisioning Out	Local File System HTTP FTP GCS via plugins S3 via plugins	[11] Local File System HTTP FTP GCS via plugins S3 via plugins	Local File System S3	No
Notifications	Yes	Yes	No	No

[1] Available in both classic and CWL Viewer modes

[2] Does not support http(s) based imports. See BioData Catalyst Limitations for limitations.

[3] Does not support http(s) based imports. See Cavatica Limitations for limitations.

[4] Does not support http(s) based imports. See CGC Limitations for limitations.

[5] Does not support some file-path based imports. See AnVIL Limitations for limitations.

[6] Does not support some file-path based imports. See BioData Catalyst Limitations for limitations.

[7] Does not support file-path or http(s) based imports. See DNAstack Limitations for limitations.

[8] Does not support some file-path based imports. See Terra Limitations for limitations.

[9] There is no launch with Galaxy button in Dockstore, but Dockstore workflows can be searched and imported from within Galaxy.

[10] All verified Dockstore WDL tools/workflows were tested successfully. However, we anticipate that more testing is needed for WDL workflows that use language features not contained within that dataset.

[11] Use the Dockstore CLI optional parameter –wdl-output-target which allows you to specify a remote path to provision output files to ex: s3://oicr.temp/testing-launcher/

Converting File-path Based Imports to Public http(s) Based Imports for WDL

See https://cromwell.readthedocs.io/en/develop/Imports/ for general knowledge on imports.

Imports allow you to reference other files in your workflow. There are two types of resources that are supported in imports: http(s) and file-path based. Any public http(s) based URL can be used as the resource for an import, such as a website, GitHub, GA4GH compliant TRS endpoint, etc.

There are times when you may want to convert file-path based imports to public http(s) imports. One such reason is to ensure compatibility with Terra since it currently does not support file-path based imports. There are many different ways to convert to a public http(s) based import, the following are two examples.

You can host your file on GitHub and import it in the workflow descriptor like this:

import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.11.0/variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl" as TopMed_variantcaller
import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/1.11.0/variant-caller/variant-caller-wdl-checker/topmed-variantcaller-checker.wdl" as checker
...

Similarly, you can also host your file on a public google bucket and import it in the workflow descriptor like this:

import "http://storage.googleapis.com/..."
...