rufus.slrm

#!/bin/bash
#$ -cwd
#$ -S /bin/bash
#SBATCH -o /scratch.global/neis/bakeoff/logs/%x_%A_%a.out
#SBATCH -e /scratch.global/neis/bakeoff/logs/%x_%A_%a.err
#SBATCH --mail-type=END,FAIL
#SBATCH -n 40
#SBATCH --mem 64G
#SBATCH --time=24:00:00

module load samtools
module load bamtools
module load bedtools

echo "Setting sample number to ${SLURM_ARRAY_TASK_ID} + ${OFFSET}"
SAMPLE_NUM=$(($SLURM_ARRAY_TASK_ID+$OFFSET))
SAMPLE=$(sed -n "${SAMPLE_NUM}p" /scratch.global/neis/bakeoff/unfinished2.txt)

echo "Sample number ${SAMPLE_NUM} is ${SAMPLE}"
# if SAMPLE directory does not exist, create it
# if [[ ! -d "/scratch.global/neis/bakeoff/${GROUP}/${SAMPLE}" && ${SAMPLE_NUM} -le ${TOTAL_SAMPLES} ]]; then
mkdir /scratch.global/neis/bakeoff/${GROUP}/${SAMPLE}
cd /scratch.global/neis/bakeoff/${GROUP}/${SAMPLE}
echo "Running RUFUS on sample ${SAMPLE}"
bash /home/pankrat2/neis/RUFUS/runRufus.sh -vs -s /scratch.global/neis/bakeoff/${GROUP}/cram/${SAMPLE}.recab.cram -cr /home/pankrat2/public/resources/GATK4/GRCh38_full_analysis_set_plus_decoy_hla.fa  -e /home/pankrat2/public/resources/RUFUS/1000G.RUFUSreference.min45.Jhash -k 25 -t 40 -r /home/pankrat2/public/resources/GATK4/GRCh38_full_analysis_set_plus_decoy_hla.fa
# else
    # echo "Directory /scratch.global/neis/bakeoff/${GROUP}/${SAMPLE} already exists or sample not found."
# fi