Map pipe test #20
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Map pipe test #20
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necrolyte2
commented
Feb 24, 2016
necrolyte2
commented
- Some fixes for some of the jip tools to normalize input
- Some fixes to make options streamable(some commands complained they could not connect output -> input without options['whatever'].streamable = True)
- map_pipe.sh + tests/jip_modules/map_pipe.jip which travis runs just to show full integration of a super simplistic mapping pipeline with our tools(needs to be expanded a bit further as we go a long)
- bwa_mem and bwa_index interconnect better now as bwa_index outputs 'ref.fasta.bwt' and bwa_index now strips the '.bwt' from the reference option input if it exists
….fasta as input. interleave_index_filter now accepts stdin correctly. paired_to_interleave removed unused forward/revese options. created simple map_pipe to simulate mapping pipeline using many of our tools to show usage as well as do integration testing
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