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Atkinson-Lab / Tractor

Scripts for implementing the Tractor pipeline
MIT License
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Add arg to zip output #9

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

These updates allow the user to pass --zip-output in the command line to write the output files to a gzipped file.

mike-w-wilson commented 3 years ago

Sorry this also adds logging statements and an ouptut path. The logger was added togive a sense of where the script is when it is running. The output path is optional but will be used as a prefix for the output files. If none is provided, the output will just be anc0.vcf.gz. I can change that to use the vcf_prefix arg by default though.

mike-w-wilson commented 3 years ago

I've added back the vcf-prefix as the default output file prefix but output-path will override this when it is provided.