Adding quinine QC functions, and quinine_pipelines (resolves #380) #381
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…enomics#210) Adds a local mode to the ADAM pipeline where Spark runs in local mode with the maximum number of cores on the machine. This requires a local-dir switch too, for pointing ADAM to the data directory.
Adds native-adam-path option to adam-pipeline.
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| # add arguments for contaimination estimation |
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…mics#380) * Adds the quinine tool (https://github.com/bigdatagenomics/quinine) along with helper functions for running QC on targeted sequencing panels, RNA-seq data, and for estimating sample contamination. * Instantiates these as command line tools in `toil_scripts.quinine_pipelines.metrics`.
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Picks up: * bigdatagenomics/quinine@a5cb6b0, fix for bigdatagenomics/quinine#34 * bigdatagenomics/quinine@be8a1b6, fix for bigdatagenomics/quinine#35, * Merge commit bigdatagenomics/quinine@2475aea * Force pushed update BD2KGenomics/toil-scripts@eed1ef8 to BD2KGenomics/toil-scripts#381.
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Picks up: * bigdatagenomics/quinine@a5cb6b0, fix for bigdatagenomics/quinine#34 * bigdatagenomics/quinine@be8a1b6, fix for bigdatagenomics/quinine#35, * Merge commit bigdatagenomics/quinine@2475aea * Force pushed update BD2KGenomics/toil-scripts@eed1ef8 to BD2KGenomics/toil-scripts#381.
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Builds on top of #351.