dockstore-workflow-md5sum

This is an extremely simple workflow used to show how to call a workflow via Dockstore.

Validation

This workflow has been validated as a CWL v1.0 launched using Dockstore 1.1.2.

Versions of dependencies that we tested include:

setuptools==28.8.0
cwltool==1.0.20161114152756
schema-salad==1.18.20161005190847
avro==1.8.1

CWL Testing

How to execute this workflow using the CWL descriptor via the Dockstore command line (which calls the cwltool command behind the scenes).

Testing Locally with the Dockstore CLI

This workflow can be found at the Dockstore, login with your GitHub account and follow the directions to setup the CLI. It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command line utility. This is great for testing.

Make a Parameters JSON

This is the parameterization of the md5sum workflow, a copy is present in this repo called Dockstore.json:

{
  "input_file": {
        "class": "File",
        "path": "md5sum.input"
    },
    "output_file": {
        "class": "File",
        "path": "/tmp/md5sum.txt"
    }
}

You will also see a Dockstore.yml file which is the same but with the "output_file" removed. This means when you run it via the Dockstore CLI you need to find the output by looking at the cwltool STDOUT e.g. look at this file:

Saving copy of cwltool stdout to: /Users/boconnor/Development/gitroot/dockstore-tool-md5sum/./datastore/launcher-002bcb21-11e2-47d4-96f5-fb542eb48bb5/outputs/cwltool.stdout.txt

This will tell you the location of the output md5sum file.

You might need to use this "output_file" free test.json if you are executing a more strict CWL execution engine like Arvados.

Run with the CWL CLI

cwltool Dockstore.cwl Dockstore.json

Run with the Dockstore CLI

Run it using the dockstore CLI locally with the Dockstore.cwl file (great for testing if you make changes locally):

# run this locally
$> dockstore workflow launch --entry Dockstore.cwl --local-entry --json Dockstore.json

Or you can run it from the latest release on Dockstore:

# run this from the Dockstore
$> dockstore workflow launch --entry briandoconnor/dockstore-workflow-md5sum:1.3.0 --json Dockstore.json

Test with travis-ci

See the .travis.yml file.

Publishing

At this point you follow the SOP from the Dockstore.org site.