pipeline.sh

#!/bin/bash
#SBATCH --job-name=mapler 
#SBATCH --time=3-00:00:00
#SBATCH --mem=5G

config=${1:-"config/config.yaml"}

if [[ "$config" == "config/config_test.yaml" ]]; then
    tar -xf "test/test_dataset.tar.gz"
fi

analysis_name=$(grep "analysis_name:" $config | cut -d " " -f 2)
timestamp=$(date +"%Y-%m-%d_%H-%M-%S")
log_directory=logs/$analysis_name/$timestamp/

# Log config file and git info
mkdir -p $log_directory
cp $config $log_directory/config.yaml
echo "Branch: $(git rev-parse --abbrev-ref HEAD)" > $log_directory/git_info.txt
echo "Latest Commit: $(git rev-parse HEAD)" >> $log_directory/git_info.txt

# Launch the pipeline
snakemake all --cores all  --executor slurm --jobs 10 \
    --printshellcmds --keep-going \
    --use-conda --rerun-triggers mtime \
    --configfile $log_directory/config.yaml \
    --default-resources mem_mb=5000 mem_mb_per_cpu=None runtime=2*60 \
    --latency-wait 60

# Get the slurm log 
cp $(scontrol show job $SLURM_JOB_ID | grep "StdOut" | awk -F "=" '{print $2}') $log_directory