unravel.utilities.process_samples module#

Use process_samples (ups) from UNRAVEL to run a command on all samples or directories containing samples.

Notes

  • {sample_path} and {sample} placeholders can be used in the command to refer to the sample directory path and name, respectively.

  • Likewise, {sp} and {s} can be used as shorthand for {sample_path} and {sample}, respectively.

Usage:#

ups -c “command” [-o rel_path/output] [-d list of paths] [-p sample??] [-v]

unravel.utilities.process_samples.parse_args()[source]#
unravel.utilities.process_samples.process_samples(command, output, dirs, pattern, verbose)[source]#

For each sample directory found by get_samples, run the user-specified command. If -o/--output is provided and already exists in the sample directory, skip processing.

unravel.utilities.process_samples.main()[source]#