Created
October 30, 2020 13:56
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| #! /bin/bash | |
| BWA_MEM_IMAGE=/juno/work/isabl/local/docker-pcapcore/v0.1.2/docker-pcapcore-v0.1.2.simg | |
| # BWA_MEM_IMAGE=/work/isabl/home/levinem1/software/containers/pcap-core_5.5.0.sif | |
| OUTDIR=`pwd`/$SAMPLE | |
| mkdir -p $OUTDIR/input_data | |
| ln -sf $INPUTDIR/input_data/*.fastq.gz $OUTDIR/input_data | |
| set -euxo pipefail | |
| bsub \ | |
| -n 32 \ | |
| -R 'rusage[mem=2]' \ | |
| -W 4000 \ | |
| -o $OUTDIR/out.logs \ | |
| singularity exec \ | |
| --workdir $TMP_DIR/${USER}_docker-pcapcore_v0.1.2_`uuidgen` \ | |
| --bind /juno:/juno \ | |
| --bind /juno/work:/work \ | |
| --bind /juno/res:/res \ | |
| ${BWA_MEM_IMAGE} bwa_mem.pl \ | |
| -outdir $OUTDIR \ | |
| -reference /work/isabl/ref/homo_sapiens/GRCh37d5/genome/gr37.fasta \ | |
| -sample $SAMPLE \ | |
| -threads 32 \ | |
| -fragment 10 \ | |
| -groupinfo $INPUTDIR/groupinfo.yaml \ | |
| -map_threads 32 \ | |
| -bwa_pl \ | |
| $OUTDIR/input_data/*.fastq.gz | |
| #! /bin/bash | |
| export SAMPLE=IID_H197214_T01_01_WG01 | |
| export INPUTDIR=/work/isabl/data/analyses/59/59/375959 | |
| sh run_bwa.sh | |
| export SAMPLE=IID_H197221_T01_01_WG01 | |
| export INPUTDIR=/work/isabl/data/analyses/70/40/377040 | |
| sh run_bwa.sh | |
| export SAMPLE=IID_H196900_T01_01_WG01 | |
| export INPUTDIR=/work/isabl/data/analyses/44/73/374473 | |
| sh run_bwa.sh | |
| export SAMPLE=IID_H196897_T01_01_WG01 | |
| export INPUTDIR=/work/isabl/data/analyses/39/22/373922 | |
| sh run_bwa.sh |
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