31 lines
765 B
Bash
31 lines
765 B
Bash
#!/bin/bash
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if [ "$#" -ne 2 ]; then
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echo "Usage: $0 <size: 1 or 3> <logfile-outname>"
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exit
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fi
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SIZE=$1
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LOGOUT=$2
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TESTDATA_ARCHIVE=/root/sarek-testdata.tar.gz
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MYDIR=$(pwd)
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mkdir -p /workspace/sarek
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mkdir -p /workspace/launch/work
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cp nextflow-k8s.config /workspace/sarek/nextflow-k8s.config
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cp runtimes.csv /workspace/launch/work/runtimes.csv
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cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
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cp samplesheet${SIZE}.csv /workspace/sarek/samplesheet.csv
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cd /workspace/launch
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tar xzf ${TESTDATA_ARCHIVE}
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cd /workspace/sarek
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time nextflow run -c nextflow-k8s.config nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
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rm -rf out
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cp .nextflow.log /${LOGOUT}
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cd ${MYDIR}
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rm -rf /workspace/*
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