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add new sarscov2_lineages workflow and travis cleanups #184

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Dec 22, 2020
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@dpark01 dpark01 commented Dec 22, 2020

Adds new sarscov2_lineages WDL workflow with two tasks: nextclade_one_sample and pangolin_one_sample. This is the first WDL code in this codebase that is species-specific (SARS-CoV-2 only) and is maintained in a separate species-specific task file.

This PR additionally does some cleanups to the Travis setup (.travis.yml, travis/ directory, etc) partly because the build was stalling and blocking tests on the above WDLs, and partly to remove some old/deprecated bits of the build that are no longer used. This should also position us well to transition to Github Actions, as the build matrix is simpler now, and only a few Travis-specific bits remain.

@dpark01 dpark01 merged commit a3bf70c into master Dec 22, 2020
@dpark01 dpark01 deleted the dp-clades branch December 22, 2020 15:40
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