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Common Workflow Language tool descriptions #39

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etal opened this issue Jul 22, 2015 · 1 comment

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etal commented Jul 22, 2015

Create CommonWL "tool" interfaces for each CNVkit sub-command. Try to use these to improve integration with Galaxy and bcbio-nextgen.

Maybe wrap "batch" as a workflow instead of a tool -- not sure how this works.

Spec: https://github.com/common-workflow-language/common-workflow-language
Examples: https://github.com/common-workflow-language/workflows

etal mentioned this issue

raise IOError("Missing CNVkit %s file: %s" % (ftype, files[ftype])) bcbio/bcbio-nextgen#915

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etal commented Jun 21, 2016 •

edited

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The interface generator gxargparse/argparse2cwl from the GSoC 2016 project automates this work, which is happening in the CWL repo: common-workflow-library/legacy#93

etal mentioned this issue

Update Galaxy tool #56

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etal mentioned this issue

Dockerize etal/cnvkit-dnanexus#3

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