gbt_pipelineΒΆ
The gbt_pipeline script is the primary driver of the pipeline. It is called after the user environment options are set by gbtpipline.
Amongst other things, gbt_pipeline does the following:
reads and interprets and logs the command line options, in part by using commandline.py
- creates a pipeline for either:
- each map in the input file when the –allmaps option is set, or
- for a single map when the beginning, end and reference scans are supplied and –allmaps is not set
