Phylogeny workflows

Installation

(First time only)

Download and install miniconda3:

For Linux:

 wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 bash Miniconda3-latest-Linux-x86_64.sh

Clone workflow to the directory where you wish to run the pipeline:
```
 git clone https://github.com/tamburinif/phylogeny_workflows
```

Create the new conda environment:

 cd phylogeny_workflows
 conda env create -f envs/environment.yaml

Conda env can be updates as follows:

    conda env update -f envs/environment.yaml

(Every time)

Activate the environment:

source activate ftools

Usage

Input files

Reference genome assembly in fasta format
Two or more short read datasets in fastq format (paired- or single-end)

Config file

You must update the config.yaml file to include the filepaths to your reference genome assembly, a list of samples, and the directory containing the input samples.

If your reads are paired-end, params 'reads1' and 'reads2' should point to directories with forward and reverse reads respectively. If working with single-end or interleaved files, point to those in 'reads1' and leave 'reads2' blank.

Running phylogeny workflow

Run as follows:

snakemake ref.tree -s Snakefile --configfile config.yaml --restart-times 1 --profile scg -j 999 --rerun-incomplete --latency-wait 10

tamburinif/phylogeny_workflows