broadinstitute / viral-ngs / 5048

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travis-ci

WDL, Cromwell, and DNAnexus auto-build (#728)

This PR adds WDL pipelines.
- The WDL pipelines are mostly inspired by the previous DNAnexus implementations of viral-ngs.
- These pipelines all execute successfully from start to finish on Cromwell via Google. I have not checked for correctness of output, but spot checking looks sane so far.
- These pipelines all compile properly to DNAnexus workflows via dxWDL (except for one, which I disabled for now, and am not sure how necessary it is to have anyway).
- None of the resulting DNAnexus workflows execute properly yet, but we'll work on that one later.
- The Travis build process now adds a few more actions in the Docker portion of the build matrix. After deploying the image to DockerHub, it rewrites the runtime sections of the WDL files to point to the versioned image, it runs a WDL validator tool on all WDL workflows, it compiles all WDL workflows to a new DNAnexus CI project, and there is a placeholder for future Cromwell tests that do not yet exist.
- The above build actions happen on every branch commit and PR, so the long-form version string tags for docker images have been re-instated.
- Bugfix to bwamem_idxstats: was previously executing bwa on un-indexed input fasta.

1 of 1 new or added line in 1 file covered. (100.0%)

5613 of 8355 relevant lines covered (67.18%)

1.34 hits per line