cegwas-nf¶
Docker image¶
The wild-isolate docker file can be used. The cegwas-nf pipeline requires R/cegwas to be installed and a python module, awesome-slugify.
Requirements¶
The cegwas-nf pipeline requires awesome-slugify; Install using:
pip install awesome-slugify
It also requires that cegwas be installed. See the cegwas repo for more information. Alternatively, you can use the wi-nf docker image.
Usage¶
# cd to directory containing a trait file.
nextflow run Andersenlab/cegwas-nf --in=<input file>
Input Format¶
Save trait data as a .tsv; Strains in column 1. Traits are in columns 2 and above.
| strain | trait1 | trait2 | trait3 | trait4 |
|---|---|---|---|---|
| AB1 | 0 | 0 | 19.6825 | 16.5026 |
| AB4 | 14.5294 | 13.9775 | 18.9721 | 20.6803 |
| BRC20067 | 18.0132 | 17.1509 | 18.4466 | 21.0243 |
| CB4855_UK | 0 | 13.2552 | 19.5265 | 21.7389 |
| CB4856 | 14.4711 | 12.2563 | 19.3584 | 21.2358 |
| CB4932 | 0 | 0 | 19.8662 | 20.326 |
| CX11254 | 17.5516 | 16.9135 | 19.5696 | 21.7276 |
| CX11264 | 15.3574 | 13.8575 | 18.9888 | 21.3832 |