#! /bin/sh ### ASDP PIPELINE ### ## pipeline.sh ## Version : 0.0.1 ## Licence : FIXME ## Description : script to launch the pipeline for STR detection ## Usage : ## Output : FIXME ## Requirements : FIXME ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Creation Date : 20191208 ## last revision date : 20191208 ## Known bugs : None SAMPLE="$1" # Check if sample is specified if [ -z "$SAMPLE" ] then echo "Sample is not specified" echo "$(date +"%F_%H-%M-%S"): END" exit 1 fi INPUTFILE="/archive/gad/shared/bam_new_genome_temp/$SAMPLE.bam" DATE="$(date +"%F_%H-%M-%S")" OUTPUTDIR="/work/gad/shared/analyse/STR/pipeline/$SAMPLE" # Transfer bam and bai from archive to work mkdir -p "$OUTPUTDIR" qsub -pe smp 1 -q transfer -N "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh INPUTFILE="$OUTPUTDIR/$SAMPLE.bam" # Launch ExpansionHunter mkdir -p "$OUTPUTDIR/eh" qsub -pe smp 4 -q batch -N "eh_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh # Launch Tredparse mkdir -p "$OUTPUTDIR/tredparse" qsub -pe smp 4 -q batch -N "tredparse_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh # Launch GangSTR mkdir -p "$OUTPUTDIR/gangstr" qsub -pe smp 4 -q batch -N "gangstr_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh # Launch ehdn profile mkdir -p "$OUTPUTDIR/ehdn" qsub -pe smp 4 -q batch -N "ehdn_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh # Delete transfered bam and bai qsub -pe smp 1 -q batch -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh