working dir for project to turn eel pond protocols (nonmodel RNAseq differential expression analysis) into a dahak-style containerized workflow

eel-pond protocols

• DIBSI, nonmodel RNAseq workshop, July 2017
• SIO-BUG, nonmodel RNAseq workshop, October 2017

Workflows:

• Read Quality Trimming and Filtering
• Digital Normalization
• Assembly
• Quality Assessment
• Annotation
• Transcript Quantification
• Differential Expression

Instructions:

Create conda env

pip install dahak-taco

Current Status:

Imported workflow style and scripts for read filtering from dahak (4-18-18). These are still under development for dahak & subject to change.

To Do:

Get dahak portion working:

• test read-filtering workflow (directly from dahak-taco)
• write installation / requirements files

Build RNAseq workflows:

• locate or write singularity recipes for all required RNA programs (e.g. Trinity, Salmon, etc)
• write snake rules for each individual program
• write Snakefile for each workflow