This is an older version of the repo please use

https://github.com/greninger-lab/Tpallidum_WGS_Pipeline

Tpallidum WGS

This pipeline is intended for assembly and annotation of Treponema pallidum whole genomes.

This pipeline takes gzipped fastq files and outputs consensus fastas annotated with Prokka. Running on the cloud is recommended due to memory-intensive mapping steps.

Installation

1. Install nextflow.
   • Make sure you move nextflow to a directory in your PATH variable.
2. Install docker.

Usage

• Example command for fastqs in current directory: nextflow run greninger-lab/Tpallidum_WGS --INPUT ./ --OUTDIR output/ -resume -with-trace -c ~/nextflow.covid.config -profile Cloud

Command	Description
--INPUT	Input folder where gzipped fastqs are located. For current directory, ./ can be used.
--OUTDIR	Output folder where .bams and consensus fastas will be piped into.
-resume	nextflow will pick up where it left off if the previous command was interrupted for some reason.
-with-docker ubuntu:18.04	Runs command with Ubuntu docker.
-with-trace	Outputs a trace.txt that shows which processes end up in which work/ folders.