09_picard_dedup_rename.srun

#!/bin/bash
#SBATCH -A phillipslab
#SBATCH --partition=phillips       ### Partition
#SBATCH --job-name=picard    ### Job Name
#SBATCH --time=10:00:00        ### WallTime
#SBATCH --nodes=1              ### Number of Nodes
#SBATCH --ntasks=1             ### Number of tasks per array job
#SBATCH --array=0-45           ### Array index
#SBATCH --cpus-per-task=1            ### Number of CPU cores per task

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

module load java samtools
picard="/projects/phillipslab/ateterina/scripts/picard/build/libs/picard.jar"

cd /projects/phillipslab/ateterina/CITP_pi/data/


LISTFILES=(*f[ps]1.fastq) 
file0=${LISTFILES[$SLURM_ARRAY_TASK_ID]}
file=${file0/_f[ps]1.fastq/.s.bam}
#LISTFILES=(*s.bam)
#file=${LISTFILES[$SLURM_ARRAY_TASK_ID]}

java -Xmx4g -jar $picard MarkDuplicates INPUT=$file OUTPUT=${file/.s.bam/.ded.bam} METRICS_FILE=${file/.s.bam/.ded.metrics.txt} REMOVE_DUPLICATES=true;

samtools index ${file/.s.bam/.ded.bam};