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Log files were moved up from these redundant directory levels, except for compress_index_VCF which is from an external process. I assume the extra level is needed in other pipelines. Perhaps within the submodule it could be renamed with something like -external. E.g. somaticsniper-external? Or an optional parameter to get rid of it?
For log level directory organization, I think we want to make a separate PR as this PR is getting bigger.
For log level directory organization, I think we want to make a separate PR as this PR is getting bigger.
Originally posted by @tyamaguchi-ucla in #183 (comment)
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