Antimicrobial Resistance Workflow

Introduction

About

This pipeline will produce the files you need for amr analysis

Pipeline

This is a diagram of the pipeline

How to install

Locally

1. clone the repo
2. install crom well and all its dependancies.

Cloud

1. open a terra account.
2. go to workflow and pick the camra wdl

Pre-work

1. open bvbrc account
2. downlaod the card database especially these files...
3. get assemblies or raw reads.

How to us

Locally

1. go to the directory you want the output.
2. run wombat validate
3. run vombat inputs
4. input the inputs
5. run cromwell run
6. the structure of the files is as follows /ccrom-e/job/..... you will find the files you are interested in in ....

Terra

1. go to the workflow pick the workflow
2. load it to your workspace.
3. pick the datatable you are getting the data from
4. populate the feild wirh the right table fields.
5. run.

Input files

Output files

Having issues

1. copy error message
2. look at stderr
3. look at stdout
4. look at term_consolidation.log
5. look at size of files.

Resources

• cromwell
• wombat

Citations