search

BIH-CEI / ERKER2Phenopackets

A pipeline of ERKER data into the phenopackets data structure.
MIT License
4 stars 1 forks source link

151 possible to call pipeline with flags #159

Closed frehburg closed 11 months ago

frehburg commented 11 months ago

https://github.com/BIH-CEI/ERKER2Phenopackets/issues/151 New usage of the pipeline command:

pipeline [-h] [-d | -t] [-p] data_path [out_dir_name]

A pipeline to map ERKER data in .csv format to phenopackets.

positional arguments:
  data_path      The path to the data
  out_dir_name   The name of the output directory

options:
  -h, --help     show this help message and exit
  -d, --debug    Enable debug logging
  -t, --trace    Enable trace logging
  -p, --publish  Write phenopackets to out instead of test
frehburg commented 11 months ago

pipeline path -> experimental pipeline -p path -> out/phenopackets