ayoraind/plasmidfinder

Nextflow pipeline utilizing plasmidfinder for in silico Inc Typing

Workflow to Utilize Plasmidfinder for Inc Typing.

Usage

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 TAPIR Plasmidfinder Pipeline version 1.0dev
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 Usage:
        The typical command for running the pipeline is as follows:
        nextflow run main.nf --input "PathTosamplesheet" --outdir "PathToOutputDir" 

        Mandatory arguments:
         --input                        Sample sheet containing 'sample' column and 'fasta' column
         --outdir                       Output directory (e.g., "/MIGE/01_DATA/plasmidfinder_out")


         Helpful arguments:
        	--help                         This usage statement.
         	--version                      Version statement

Introduction

This pipeline uses Plasmidfinder to predict plasmid Inc Types.

Word of Note

This is an ongoing project at the Microbial Genome Analysis Group, Institute for Infection Prevention and Hospital Epidemiology, Üniversitätsklinikum, Freiburg. The project is funded by BMBF, Germany, and is led by Dr. Sandra Reuter.

Authors and acknowledgment

The TAPIR (Track Acquisition of Pathogens In Real-time) team.