broadinstitute / viral-ngs / 5208

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travis-ci

WDL, dx, and build updates (#732)

- update Docker base image from `docker.io/broadinstitute/viral-baseimage:0.1.5` to `quay.io/broadinstitute/viral-baseimage:0.1.6`
- Update the Dockerfile build to no longer rely on the large easy-deploy script, and instead to just invoke the simple `conda install` lines directly. Break up the monolithic `conda install` Docker layer into two relatively equal sized layers, which seems to *sometimes* provide a faster `docker pull` for some clients. (I had previously also attempted to install only a minimal set of conda tools and let the `Tool` self-installer code dynamically install tools as needed, but this appears to no longer work in more complicated scenarios with multiple conda packages that depend on each other, e.g. bmtagger, so this effort was abandoned)
- move production and dev docker repos to `quay.io`, which provides faster `dx-docker pull` for DNAnexus, and is an all around nicer web UI to work with than DockerHub, and provides future possibilities to play with `rkt`, squashed images, and bittorrent pulls (though I am increasingly skeptical that that will matter).
- move DNAnexus Travis CI project to a new one created by the DNAnexus Science Team, which was the only way to make it a Public DNAnexus project.
- update documentation all around to reflect build process changes
- WDL pipelines: add a `refine_2x_and_plot task` which is simply an optimization around the refine, refine, plot_coverage tasks at the end of all assembly workflows. The original atomic tasks are still available, but this saves a lot of staging time for routine analyses.
- WDL scaffolding step: implemented @notestaff 's recent improvements to `order_and_orient` which allows the user to provide multiple reference genomes for this stage. Also, the WDL task now extracts more metrics and outputs from this stage that might be useful.
- taxon_filter.py: some further clean up and optimization around blastn read depletion. Also revert the... (continued)

169 of 169 new or added lines in 4 files covered. (100.0%)

6042 of 8520 relevant lines covered (70.92%)

0.71 hits per line