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Running Common Workflow Language (CWL) workflows on Arvados » History » Version 4

Peter Amstutz, 03/03/2016 07:04 PM

1 1 Peter Amstutz
h1. Running Common Workflow Language (CWL) workflows on Arvados
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"Common Workflow Language (CWL)":http://commonwl.org is an emerging standard for describing portable, cross-platform workflows.  The Arvados project has been involved in this effort from the very beginning, and is pleased to offer preliminary support for running CWL in Arvados.
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The Arvados CWL runner is located at "arvados/sdk/cwl" in the Arvados source tree.  The Python package is called "arvados-cwl-runner".  You can also install from PyPi:
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<pre>
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$ pip install arvados-cwl-runner
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</pre>
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If you are using a shell account on a Curoverse-hosted cluster, your environment is already set up.  Otherwise, first "set up your environment":http://doc.arvados.org/user/reference/api-tokens.html (see also [[Arvswitch]] to help manage your Arvados credentials.)
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If a pipeline inputs refer to local files, they will be uploaded before running the pipeline.  You can also reference files already in Keep by prefixing "keep:" for example "keep:d341a6f1db391a780d694e240e95e475+3805/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta".
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See the "lobSTR":https://github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/ pipeline for an example.