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#!/bin/bash
#PBS -l walltime=48:00:00
#PBS -l ncpus=16,mem=8gb
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#PBS -N trio_whole_exome_bcbio
#PBS -j oe
# enable running singletons
if [ -z $PBS_ARRAY_INDEX ]
then
if [ -z $INDEX ]
then
export PBS_ARRAY_INDEX=1
else
export PBS_ARRAY_INDEX=$INDEX
fi
fi
# Expects environment variables to be set
# PROJECT_ID - e.g. 12345_LastnameFirstname
# CONFIG_SH - absolute path to configuration script setting environment variables
source $CONFIG_SH
FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
CONFIG_FILE=$CONFIG_DIR/${PROJECT_ID}_${FAMILY_ID}.yaml
mkdir -p $WORK_DIR/$FAMILY_ID
cd $WORK_DIR/$FAMILY_ID
bcbio_nextgen.py $CONFIG_FILE -n 16 -t local
DATE=$(basename `tail log/bcbio-nextgen.log | grep 'Storing in local filesystem' | tail -n 1 | awk '{ print $6 }' | perl -pe "s/_${PROJECT_ID}.+//"`)
if [ -e $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} ]
then
for INDV in `cut -f 2 $PARAMS_DIR/${PROJECT_ID}_${FAMILY_ID}.ped`
do
mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}/
done
# fix VCF output file names
cd $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}
if [ ! -e ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz ]
PREFIX=`echo $FAMILY_ID | cut -d '_' -f 1`
SUFFIX=`echo $FAMILY_ID | cut -d '_' -f 2`
mv ${PREFIX}${SUFFIX}-gatk-haplotype-annotated.vcf.gz ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz
mv ${PREFIX}${SUFFIX}-gatk-haplotype-annotated.vcf.gz.tbi ${FAMILY_ID}-gatk-haplotype-annotated.vcf.gz.tbi