chanjo integration. Fix for #494 #500
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…c/environment bcbio#497. Ensure bcbio symlinked into PATH when doing upgrades
| sample_name = tz.get_in(['rgnames','sample'], data[0], None) | ||
| bed_file = tz.get_in(["config", "algorithm", "coverage"], data[0], None) | ||
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| outport_dir = os.path.abspath(tz.get_in(['upload', 'dir'], data[0])) |
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Minor spelling correction: should be "output"
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John -- thanks much for this work in progress. It's all merged in and looking forward to seeing how it goes moving forward with the new chanjo API changes. Great work. |
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Here is the integration with Chanjo. It was tested using the test only ChanjoPipeline
Also, this includes a fix for #494. A unit test is provided.
-jk