dahak-flot

This repository contains files for Snakemake workflows for dahak.

(flot is French for flow.)

You should start with a version of conda installed.

See snakemake-rules repo for example Snakefile rules and guiding principles.

Quick Start: Taxonomic Classification

(Example target file? Test?)

Getting Started

This document walks you through running Snakemake workflows:

GettingStarted.md

General Notes: How This Repo Is Organized

This document covers how Snakemake rules and files are organized:

Organized.md

Customizing

Snakemake rules can use their own conda environments. To do this, add your conda environmnent .yml to the envs/ directory.

To add or modify the rules, determine the name of the step you wish to modify, and find it in the rules/ directory.

To view or modify the file containing taxonomic classification workflow settings, edit taxclass.settings.

To define your own settings for Snakemake to use, see user.settings.