sanger-pathogens/update_pipeline — pull request #21 by jm23 (2012-06-07 14:07:22+00:00)
Title: Changes for vertres tracking pipeline

New flags:
-t (taxon_id) -> provide taxon id to overwrite species info in bam file common name.

-l (use_supplier_name) -> use the supplier name from the warehouse to populate name and hierarchy name of the individual table.

-i (specific_run_id) -> provide a specfic run id for a study (data security issues...).

Change to IRODS::File to retrieve the md5 using ichksum if it's missing from the bam metadata