├── .gitignore ├── MGERT.py ├── README.md ├── config ├── config.yaml └── samples.tsv ├── envs ├── bedtools.yaml ├── repeatmasker.yaml └── repeatmodeler.yaml ├── images ├── flowchart.png └── hist.png ├── install.sh ├── test_dataset.tgz └── workflow ├── Snakefile └── scripts ├── __init__.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/.gitignore -------------------------------------------------------------------------------- /MGERT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/MGERT.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/README.md -------------------------------------------------------------------------------- /config/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/config/config.yaml -------------------------------------------------------------------------------- /config/samples.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/config/samples.tsv -------------------------------------------------------------------------------- /envs/bedtools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/envs/bedtools.yaml -------------------------------------------------------------------------------- /envs/repeatmasker.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/envs/repeatmasker.yaml -------------------------------------------------------------------------------- /envs/repeatmodeler.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/envs/repeatmodeler.yaml -------------------------------------------------------------------------------- /images/flowchart.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/images/flowchart.png -------------------------------------------------------------------------------- /images/hist.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/images/hist.png -------------------------------------------------------------------------------- /install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/install.sh -------------------------------------------------------------------------------- /test_dataset.tgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/test_dataset.tgz -------------------------------------------------------------------------------- /workflow/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/workflow/Snakefile -------------------------------------------------------------------------------- /workflow/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /workflow/scripts/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andrewgull/MGERT/HEAD/workflow/scripts/utils.py --------------------------------------------------------------------------------