A script to submit a SLURM job to run Bactopia Tools on ATB data

mbow-bactopia-tool-atb

#! /bin/bash
# A script to submit a SLURM job to run Bactopia Tools on ATB data
# Expected Options:
# 1: Bactopia directory
# 2: Bactopia Tool
# 3: config file
# 4: A specific profile to use
# 5: A specific account to use
# 6: Where to cache singularity/apptainer images
BACTOPIADIR=${1}
WF=${2}
NFCONFIG=${3:-"/home/rpetit/bin/mbow.config"}
PROFILE=${4:-"mbow_fast"}
SBATCH_ACCOUNT=${5:-"healthdatasci"}
NXF_SINGULARITY_CACHEDIR=${6:-"/gscratch/rpetit/singularity-cache"}

sbatch <<EOT
#!/bin/bash
#SBATCH --job-name=bactopia-atb-${WF}
#SBATCH --output=bactopia-atb-${WF}.out
#SBATCH --error=bactopia-atb-${WF}.err
#SBATCH --time=72:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --account=${SBATCH_ACCOUNT}
#SBATCH --qos=Normal

# Load the necessary modules
module load miniconda3
module load apptainer
conda activate bactopia

export NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR}
export SBATCH_ACCOUNT=${SBATCH_ACCOUNT}

# Change to the working directory
bactopia \
    --bactopia ${BACTOPIADIR} \
    --wf ${WF} \
    --nfconfig ${NFCONFIG} \
    -profile ${PROFILE} \
    -resume
EOT