🚰 Snakemake files for dahak workflows.

Charles Reid 8da83409ca Merge branch 'master' of github.com:charlesreid1/dahak-flot 3 days ago
cloud Removing cloud from dahak-flot (see dahak-bespin) 3 days ago
envs Move basic environment yml file 1 week ago
inputs Verified snakefile up to sourmash step. 1 week ago
rules Moving rules to own directory 1 week ago
.gitignore Verified snakefile up to sourmash step. 1 week ago
GettingStarted.md update dahak-yeti links 3 days ago
LICENSE 2 legit 2 init commit 3 weeks ago
Organized.md updating organized readme 1 week ago
README.md adding info on how to customize the snakemake workflow 3 days ago
Snakefile Updating Snakefile onsuccess rule 3 days ago
bootstrap.sh bootstrap our way to Snakemake 1 week ago
taxclass.settings Add test script, get Snakefile successfully parsed 1 week ago
test_snake.sh add kaiju2krona test 1 week ago
user.settings add sample user settings file 1 week ago



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:


General Notes: How This Repo Is Organized

This document covers how Snakemake rules and files are organized:



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.