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Document command-line args required by pipeline COMMAND

Open hammer opened this issue 9 years ago • 1 comments

When I run KETREW_CONFIG=./ketrewdocker/configuration.ml ocaml jh-epidisco.ml pipeline --help I am greeted with a wonderful list of arguments; given a stratotemplate setup, could we also document some good default values for these parameters?

hammer avatar Aug 09 '16 02:08 hammer

Currently running over @smondet's private DREAM chr20 BAMs: KETREW_CONFIG=./ketrewdocker/configuration.ml ocaml jh-epidisco.ml pipeline -E jh-epidisco-test --results-path /nfswork/jh-epidisco-test --reference-build=b37 --normal /nfstest1/datasets/training-dream/normal.chr20.bam --tumor /nfstest1/datasets/training-dream/tumor.chr20.bam

hammer avatar Aug 09 '16 03:08 hammer