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pharmAnnot
Commit 3c5a5a82 authored by Simon Verdez's avatar Simon Verdez
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pipeline works

parent 5f8e477e
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Showing with 19 additions and 10 deletions
Master.sh
View file @ 3c5a5a82
......@@ -66,7 +66,7 @@ PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2`
OMIM=`grep "omim" $PHARMCONFIG | cut -f2`
HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2`
HEADER=`grep "header" $PHARMCONFIG | cut -f2`
REF=`grep "reference" $PHARMCONFIG | cut -f2`
# python path for proper execution of python
PYTHONPATH=$PIPELINEBASE/common:/work/gad/shared/bin/lib/python_2.7/lib/python2.7/site-packages:/work/gad/shared/bin/miniconda2/lib/python2.7/site-packages/
......@@ -104,11 +104,11 @@ else
fi
# get the status
REF=`grep "reference" $STATUSFILE | cut -f2`
HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2`
varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2`
varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2`
createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2`
mergeVCF=`grep "mergeVCF" $STATUSFILE | cut -f2`
if [ "$HLAscan" == "FAIL" ]
then
......@@ -139,6 +139,14 @@ else
echo "CreateHTML step was OK"
fi
if [ "$mergeVCF" == "FAIL" ]
then
echo "MergeVCF step failed : jumping to merge step"
jumpto MergeVCF
else
echo "MerfeVCF step was OK"
fi
echo "pipeline was correctly executed, no need to relaunch a step"
exit 0
fi
......@@ -172,7 +180,7 @@ echo "### Execute HLAscan ###"
echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples
do
echo "Command : qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,OUTPUTFILE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh"
echo "Command : qsub -pe smp 2 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,OUTPUTFILE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh"
qsub -pe smp 1 -N HLAscan_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v BAM=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,SORTIE=$ANALYSISDIR/$currentSample/HLAscan,GeneList=$GL,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_HLAscan.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/haplo_scan.sh
done
echo "End : $(date +"%F_%H-%M-%S")"
......@@ -208,8 +216,8 @@ echo "### Generate HTML report ###"
echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples
do
echo "Command : qsub -pe smp 1 -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh"
qsub -pe smp 1 -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCFFILE_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCFFILE_CNV=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/$currentSample.report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh
echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh"
qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample},HLAscan_${currentSample} -N createHTML_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v VCF_SNP=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,VCF_CNV=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,REPORTFILE=$ANALYSISDIR/$currentSample/HLAscan/Report,BAMFILE=$ANALYSISDIR/$currentSample/$currentSample.dedup.bam,TSVFILE=$TSVFILE,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.html,LOGFILE=$ANALYSISDIR/$currentSample/logs/create_html.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_create_html.sh
done
echo "End : $(date +"%F_%H-%M-%S")"
......@@ -219,7 +227,7 @@ echo "### Merge VCF files"
echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples
do
echo "Command : qsub -pe smp 1 -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh"
qsub -pe smp 1 -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcall.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh
echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh"
qsub -pe smp 1 -hold_jid varcallCNV_${currentSample},varcallSNP_${currentSample} -N mergeVCF_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE1=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,INPUTFILE2=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh
done
echo "End : $(date +"%F_%H-%M-%S")"
create_html.py 0 → 100755
View file @ 3c5a5a82
This diff is collapsed.
merge_GATK.sh
View file @ 3c5a5a82
......@@ -81,10 +81,10 @@ fi
JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
PATHSCRIPT=$(grep "pipelinebase" $CONFIGFILE | awk '{print $2}')
GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
#GATK=$(grep "GATKbase" $CONFIGFILE | awk '{print $2}')
echo "command : $JAVA -jar $GATK -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY"
$JAVA -jar $GATK -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE
echo "command : $JAVA -jar /work/gad/shared/bin/GATK_3.8/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE1 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY"
$JAVA -jar /work/gad/shared/bin/GATK_3.8/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE
genotypeMerge_exitcode=$?
echo "GenotypeMerge exit code : $genotypeMerge_exitcode"
......
pharmconfig.tsv
View file @ 3c5a5a82
......@@ -3,3 +3,4 @@ pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
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