# Genome Genie

Quick and easy varaint calling and/or gene count expression pipeline

Just dump your fastq files into the "fastq_files" folder and run!

Notes

Will require download of a google drive or dropbox resource folder (work in progress)
(Pipeline is still being built out)

Currently produces:

• VCF files
• RNAseq count tables and differential expression analysis

Build docker image

docker build -t bio-pipeline .  

Run (for docker windows)

docker run -it -d `
  --mount type=bind,source="$(pwd)/fastq_files",target=/BIP/fastq_files `
  --mount type=bind,source="$(pwd)/outputs",target=/BIP/outputs `
  --mount type=bind,source="$(pwd)/resources",target=/BIP/resources `
  --mount type=bind,source="$(pwd)/scripts",target=/BIP/scripts `
  --mount type=bind,source="$(pwd)/subworkflow",target=/BIP/subworkflow `
  bio-pipeline bash

Calling different workflows

Use snakemake config arguments

For variant calling pipeline:

snakemake --config run_variant_calling=True -j {cores}

For RNAseq count matrix:

snakemake --config run_gene_quantification=True -j {cores}

For differential expression:
Will require samplesheet grouping (work in progress)