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run_hlamapper.slurm
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run_hlamapper.slurm
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#!/usr/bin/bash
#SBATCH -N 1
#SBATCH -c 8
#SBATCH --mem=128gb
#SBATCH --time=24:00:00
#SBATCH -p bch-largemem
#SBATCH --array=2
#SBATCH --job-name=hla-mapper
#SBATCH [email protected]
#SBATCH --mail-type=END,FAIL
#SBATCH -o /temp_work/ch229163/log/hla-mapper.%A-%a
source /programs/biogrids.shrc
export STAR_X=2.7.9a
export SAMTOOLS_X=1.17
HLAMAPPER=/lab-share/IM-Gutierrez-e2/Public/vitor/software/hla-mapper/ver_4.3/bin/linux_64/hla-mapper
DB=/lab-share/IM-Gutierrez-e2/Public/vitor/software/hla-mapper/ver_4.3/db/hla-mapper_db_004.3_HLA
# INPUT
META=${SLURM_SUBMIT_DIR}/sample_description.tsv
SAMPLE=$( awk -v ARRID="$SLURM_ARRAY_TASK_ID" 'FNR==ARRID { print $1 }' $META )
BAM=${SLURM_SUBMIT_DIR}/mapping/${SAMPLE}_Aligned.sortedByCoord.out.bam
OUT=${SLURM_SUBMIT_DIR}/hla-mapper/${SAMPLE}
$HLAMAPPER rna \
bam=$BAM \
sample=$SAMPLE \
threads=$SLURM_CPUS_PER_TASK \
db=$DB \
output=$OUT