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