module type Compiler_configuration = sig .. end
val work_dir : string
Directory where all work product done by the TTFI end up.
val results_dir : string option
Directory where `save` files will end up.
val machine : Biokepi_run_environment.Machine.t
Biokepi machine used by the TTFI workflow.
val map_reduce_gatk_indel_realigner : bool
Whether or not to scatter-gather the indel-realigner results.
val input_files : [ `Copy | `Do_nothing | `Link ]
What to do with input files: copy or link them to the work directory, or
do nothing. Doing nothing means letting some tools like "samtools sort"
write in the input-file's directory.