A snakemake repository that can be used for GMS collaborations.
An example of a simple workflow that will perform trimming, alignment and stats generation.
Setup (see exmaple_files):
- Create a samples.tsv file
- Create units.tsv file
- create/setup config.yaml file
virtualenv -p python3 venv
source venv/bin/activate
# Install python dependencies
pip install -r path/gms_somatic/requirements.txt
# Build singularity image with required softwares
singularity build basic.simg basic.def
# Run snakemake
snakemake -j 128 \
-s /path/projects/software/gms_somatic/basic.Snakefile \
--directory /path/projects/gms_project \
--use-singularity --singularity-args "--bind /data --bind /path "