Skip to content

Swart-lab/loxodes-assembly-workflow

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

90 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Snakemake workflow for Loxodes genomics project

Snakefiles and Conda environment definition files for the Loxodes genomics project. The top level Readme for this project is README_root.md, which documents the folder structure of the main storage project folder.

These files should reside in a subfolder workflow of the main storage project. The Snakemake pipeline is called from there, so the paths in Snakemake rules are relative to the enclosing folder.

The main Snakefile is called Snakefile, and rules for discrete tasks are organized into separate Snakefiles that are included in the main Snakefile. This is to limit the size of individual Snakefiles to make them less unwieldy.

Some steps, e.g. assembly with Falcon, were not included as Snakefiles because these require manual intervention or checking between steps, not suitable for automation. For purposes of version control the scripts responsible are included in the scripts/ subfolder, and documented with READMEs in each folder.