samesense/fq-splitter repository overview

# clone this repo
git clone https://github.com/samesense/fq-splitter/

cd fq-splitter

# mk tmp dir
mkdir tmp

# stage example files
mkdir -p data/raw/fq_gz/
cp data/test/*fq.gz files to data/raw/fq_gz/

# adjust configs/mac_test_run.config

# enter docker container; mount your local path to external
# your local path is one dir above fq-splitter (ex. /your/local/path/fq-splitter/)
docker run -it -v /your/local/path/:/external/ \
--privileged=True --cap-add=SYS_ADMIN --detach-keys="ctrl-@" \
samesense/fq-splitter

conda activate split-fq
cd /external/fq-splitter/

# run pipeline
snakemake -s src/rules/Snakefile.py \
--use-singularity --singularity-args "-B /external:/external" \
--configfile configs/mac_test_run.config all