card_rgi

Purpose

This component performs anti-microbial gene screening using CARD rgi. It uses data from CARD database.

Note

Software page: https://github.com/arpcard/rgi

Input/Output type

  • Input type: Fasta
  • Output type: None

Note

The default input parameter for fasta data is --fasta.

Parameters

  • alignmentTool: Specifies the alignment tool. Options: DIAMOND or BLAST

Published results

  • results/annotation/card_rgi: Stores the results of the screening for each sample.

Published reports

None.

Default directives

  • container: flowcraft/card_rgi
  • version: 4.0.2-0.1