Nextflow Pipeline to Run Non-Model Organism Gene Family Evolution With CAFE

This pipeline takes a selection of NCBI refseq IDs and denovo genomes, and identifies gene expansions and contractions across a phylogeny by running CAFE (Computational analysis of family evolution). This github repository is forked version of the main pipeline: https://github.com/chriswyatt1/Goatee

Important Files to View

1) Refined_species.csv: This is the input file I used to run this pipeline 2) Main.alt.nf: This is the central nextflow script that defines the workflow

How I ran this pipeline

I ran the pipeline with a mix of denovo genomes and NCBI refseq IDs

nextflow run main.alt.nf -resume -profile myriad -bg --input Refined_species.csv

There are a number of outputs from running this pipeline

CAFE_summary.csv: This is an example of one of the outputs from this pipeline

We can add modules to this

We can add novel modules such as GO analysis and more precise annotation of genes.