run.all.scripts: Run all the generated bash scripts without HPC commands
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Run all the scripts generated by previous parts of the pipeline, without using HPC commands

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run.all.scripts(output.directory, stages.to.run = c("alignment", "qc",
  "calling", "annotation", "merging"), variant.callers = NULL,
  quiet = FALSE)

`output.directory`	Main directory where all files should be saved
`stages.to.run`	A character vector of all stages that need running
`variant.callers`	A character vector of variant callers to run
`quiet`	Logical indicating whether to print commands to screen rather than submit jobs. Defaults to FALSE, can be useful to set to TRUE for testing.