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Ran 13 Nov 2017 03:52PM UTC

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Committed 13 Nov 2017 03:32PM UTC coverage: 67.175% (+0.3%) from 66.845%

Job # PERFORM_TESTING=true

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

misc fixes, optimizations, and WDL WiP (#716)

Included in this PR:

- move `--threads` argparse option to `util.cmd.common_args`
- some travis cleanup re: pip package installs
- travis/deploy-docker.sh bugfix (PR builds were overwriting `broadinstitute/viral-ngs:latest` even before merging the PR)
- a bit of optimizations in `illumina_demux`
- add `set -e -o pipefail` to `kraken.pipeline`
- some new features in `deplete_bmtagger_bam` and `deplete_blastn_bam`: can now accept blast/bmtagger databases as `.tar.gz`, `.tar.lz4`, `.tar.bz2` bundles and also as unindexed fasta files (that will be indexed on the fly)
- new internal function `util.file.extract_tarball` also exposed on the CLI as `read_utils.py extract_tarball`. Accepts stdin piped input.
- adds the new `lz4-bin`, `pigz`, and `lbzip2` packages to `requirements-conda.txt`

And also...
- WiP: initial work for WDL & Cromwell support in pipelines.. (don't review this too deeply--not quite production ready yet, but just getting the main pieces in place)

Run Details

5589 of 8320 relevant lines covered (67.18%)

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