/gms_somatic

Placeholder for solid tumor bioinformatic workflow

MIT LicenseMIT

gms_somatic workflow

A snakemake repository that can be used for GMS collaborations.

workflows

basice workflows

An example of a simple workflow that will perform trimming, alignment and stats generation.

How to run

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  "