Create wrapper for ExpansionHunter

parents
*~
*.bam
*.bai
\ No newline at end of file
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_expansionhunter.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing ExpansionHunter script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191102
## Known bugs : None
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_expansionhunter.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing ExpansionHunter script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=/path/to/the/matrix/file>,OUTPUTDIR=</path/to/the/output/dir>,[BASENAME=analysis_basename],[TESTTYPE=et|qlf|lrt],[LOGFILE=/path/to/the/log/file],[CONFIGFILE=/path/to/the/config/file] wrapper_expansionhunter.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191102
## Known bugs : None
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=expansionhunter.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> "$LOGFILE" 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exists
if [ ! -f "$INPUTFILE" ]
then
echo "Input file does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch expansionhunter.failed
exit 1
fi
# Check if output prefix is specified
if [ -z "$OUTPUTPREFIX" ]
then
echo "Output prefix is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch expansionhunter.failed
exit 1
fi
# Create .bam and .bai symbolic links
TMPDIR="$(mktemp -d)"
ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFLE")"
ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
#FIXME TODO create a pipeline to launch the qsub script
#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bam ./dijen017.bam
#ln -s /archive/gad/shared/bam_new_genome_temp/dijen017.bai ./dijen017.bam.bai
# Launch script command and check exit code
echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
--reads "$TMPDIR/$(basename "$INPUTFLE")" \
--reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
--output-prefix "$OUTPUTPREFIX""
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
--reads "$TMPDIR/$(basename "$INPUTFLE")" \
--reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
--output-prefix "$OUTPUTPREFIX"
expansionhunter_exitcode=$?
# Remove .bam and .bai symbolic links
rm "$TMPDIR/$(basenam e"$INPUTFILE")"
rm "$TMPDIR/$(basename "$INPUTFILE").bai"
rmdir "$TMPDIR"
echo "expansionhunter exit code : $expansionhunter_exitcode"
if [ $expansionhunter_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch expansionhunter.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
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