Added bowtie2 and SNAP aligners (resolves #102) #105
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jvivian
approved these changes
Aug 14, 2017
| def run_bowtie2(job, | ||
| read1, | ||
| name1, name2, name3, name4, rev1, rev2, ref, | ||
| read2=None): |
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Is this being called directly from the tool that generates the index files? It might be a bit cleaner to pass a dict of IDs, but if you'd prefer it this way that's fine.
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I am OK either way. Let me know if you have strong preferences.
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Actually, I've been thinking about this more (i.e., actually wiring up the tools) and you're correct. I'll be refactoring this shortly.
| '-o', '-bam', '/data/sample.bam', | ||
| '-t', str(job.cores)] | ||
| else: | ||
|
|
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You think whitespace is free or something?
| if not sort: | ||
| return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'sample.bam')) | ||
| else: | ||
| return (job.fileStore.writeGlobalFile(os.path.join(work_dir, 'sample.bam')), |
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Minor: outermost parentheses unnecessary as more than one item is always returned as a tuple.
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