dryrun_snakemake.bash

#!/usr/bin/env bash

#$ -cwd
#$ -r n
#$ -V
#$ -l h_vmem=2G
#$ -j y

#Uncomment the next two lines if you want to 'qsub' this script
source ~/.bashrc #needed to make "conda" command to work
conda activate qiime2-snakemake

set -xeuo pipefail

if [ $# -ne 1 ]; then
    echo "Usage: bash $0 PATH_TO_CONFIG"
    exit 1
fi

CONFIG_FP=$1

snakemake \
    --jobs 100 \
    --configfile ${CONFIG_FP} \
    --cluster-config cluster.json \
    --keep-going \
    --latency-wait 90 \
    --notemp \
    --printshellcmds \
    --cluster \
    "qsub -cwd -r n -V -l h_vmem={cluster.h_vmem} -l mem_free={cluster.mem_free} -pe smp {threads}" \
    --dryrun