#!/bin/bash
#SBATCH -J GTDB-Tk               # Job name
#SBATCH -o /work/<<UID>>/job.%j.out   # Name of stdout output file (%j expands to jobId)
#SBATCH -e /work/<<UID>>/job.%j.err   # Name of stderr output file (%j expands to jobId)
#SBATCH -n 16                 # Total number of threads requested or total number of mpi tasks
#SBATCH --mem=32000           # Maximum amount of memory in Mb the job can use
#SBATCH -t 02:00:00           # Run time ([d-]hh:mm:ss) - 1.5 hours
#SBATCH --mail-type=ALL
#SBATCH --mail-user=your.email@wur.nl

# Load your software/command
module load apptainer/1.5.2

# Run your command
GTDBTK_DATA_PATH="/work/databases/gtdb/release_232"
CONTAINER=/tools/containers/gtdbtk_272.sif

apptainer run \
  --bind /work/${USER}:/data \
  --bind ${GTDBTK_DATA_PATH}:/refdata \
  ${CONTAINER} \
  classify_wf --genome_dir /data/genomes --out_dir /data/output