flowcraft.templates.pATLAS_consensus_json module

Purpose

This module is intended to generate a json output from the consensus results from all the approaches available through options (mapping, assembly, mash screen)

Expected input

The following variables are expected whether using NextFlow or the main() executor.

• mapping_json : String with the name of the json file with mapping results.

  • e.g.: 'mapping_SampleA.json'

• dist_json : String with the name of the json file with mash dist results.

  • e.g.: 'mash_dist_SampleA.json'

• screen_json : String with the name of the json file with mash screen results.

  • e.g.: 'mash_screen_sampleA.json'

Code documentation