How to process a list of files with SLURM - bash

Question

I'm new to SLURM. I want to process a list of files assembled_reads/*.sorted.bam in parallel. With the code below, however only one process is being used over and over again.
#!/bin/bash
#
#SBATCH --job-name=****
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH --partition=short
#SBATCH --time=12:00:00
#SBATCH --array=1-100
#SBATCH --mem-per-cpu=16000
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=****#***.edu
srun hostname
for FILE in assembled_reads/*.sorted.bam; do
echo ${FILE}
OUTFILE=$(basename ${FILE} .sorted.bam).raw.snps.indels.g.vcf
PLDY=$(awk -F "," '$1=="$FILE"{print $4}' metadata.csv)
PLDYNUM=$( [[$PLDY = "haploid" ]] && echo "1" || echo "2")
srun java -Djava.io.tmpdir="tmp" -jar GenomeAnalysisTK.jar \
-R scaffs_HAPSgracilaria92_50REF.fasta \
-T HaplotypeCaller \
-I ${${SLURM_ARRAY_TASK_ID}} \
--emitRefConfidence GVCF \
-ploidy $PLDYNUM \
-nt 1 \
-nct 24 \
-o $OUTFILE
sleep 1 # pause to be kind to the scheduler
done

Answer 1

You are creating a job array but are not using it. You should replace the for-loop with an indexing of the files based on the slurm job array id:
#!/bin/bash
#
#SBATCH --job-name=****
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH --partition=short
#SBATCH --time=12:00:00
#SBATCH --array=0-99
#SBATCH --mem-per-cpu=16000
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=****#***.edu
srun hostname
FILES=(assembled_reads/*.sorted.bam)
FILE=${FILES[$SLURM_ARRAY_TASK_ID]}
echo ${FILE}
OUTFILE=$(basename ${FILE} .sorted.bam).raw.snps.indels.g.vcf
PLDY=$(awk -F "," '$1=="$FILE"{print $4}' metadata.csv)
PLDYNUM=$( [[$PLDY = "haploid" ]] && echo "1" || echo "2")
srun java -Djava.io.tmpdir="tmp" -jar GenomeAnalysisTK.jar \
-R scaffs_HAPSgracilaria92_50REF.fasta \
-T HaplotypeCaller \
-I ${${SLURM_ARRAY_TASK_ID}} \
--emitRefConfidence GVCF \
-ploidy $PLDYNUM \
-nt 1 \
-nct 24 \
-o $OUTFILE
Just make sure to adapt the value of --array to be equal to the number of files to process.