Create wrapper for ExpansionHunter

.gitignore

+*~
+*.bam
+*.bai
\ No newline at end of file

launch_expansionhunter.sh

+#! /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

wrapper_expansionhunter.sh

+#! /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"
+
+
+
+
+