Commit 3c5a5a82 authored by Simon Verdez's avatar Simon Verdez

pipeline works

parent 5f8e477e
...@@ -66,7 +66,7 @@ PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2` ...@@ -66,7 +66,7 @@ PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2`
OMIM=`grep "omim" $PHARMCONFIG | cut -f2` OMIM=`grep "omim" $PHARMCONFIG | cut -f2`
HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2` HLALIST=`grep "HLAlist" $PHARMCONFIG | cut -f2`
HEADER=`grep "header" $PHARMCONFIG | cut -f2` HEADER=`grep "header" $PHARMCONFIG | cut -f2`
REF=`grep "reference" $PHARMCONFIG | cut -f2`
# python path for proper execution of python # python path for proper execution of python
PYTHONPATH=$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/ 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 ...@@ -104,11 +104,11 @@ else
fi fi
# get the status # get the status
REF=`grep "reference" $STATUSFILE | cut -f2`
HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2` HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2`
varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2` varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2`
varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2` varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2`
createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2` createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2`
mergeVCF=`grep "mergeVCF" $STATUSFILE | cut -f2`
if [ "$HLAscan" == "FAIL" ] if [ "$HLAscan" == "FAIL" ]
then then
...@@ -139,6 +139,14 @@ else ...@@ -139,6 +139,14 @@ else
echo "CreateHTML step was OK" echo "CreateHTML step was OK"
fi fi
if [ "$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" echo "pipeline was correctly executed, no need to relaunch a step"
exit 0 exit 0
fi fi
...@@ -172,7 +180,7 @@ echo "### Execute HLAscan ###" ...@@ -172,7 +180,7 @@ echo "### Execute HLAscan ###"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N HLAscan_${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 $PIPELINEBASE/haplo_scan.sh qsub -pe smp 1 -N HLAscan_${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 done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
...@@ -208,8 +216,8 @@ echo "### Generate HTML report ###" ...@@ -208,8 +216,8 @@ echo "### Generate HTML report ###"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N createHTML_${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 $PIPELINEBASE/wrapper_create_html.sh" echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${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 $PIPELINEBASE/wrapper_create_html.sh"
qsub -pe smp 1 -N createHTML_${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 $PIPELINEBASE/wrapper_create_html.sh qsub -pe smp 1 -hold_jid varcallCNV_${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 done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
...@@ -219,7 +227,7 @@ echo "### Merge VCF files" ...@@ -219,7 +227,7 @@ echo "### Merge VCF files"
echo "Start : $(date +"%F_%H-%M-%S")" echo "Start : $(date +"%F_%H-%M-%S")"
for currentSample in $samples for currentSample in $samples
do do
echo "Command : qsub -pe smp 1 -N mergeVCF_${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 $PIPELINEBASE/merge_GATK.sh" echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${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 $PIPELINEBASE/merge_GATK.sh"
qsub -pe smp 1 -N mergeVCF_${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 $PIPELINEBASE/merge_GATK.sh qsub -pe smp 1 -hold_jid varcallCNV_${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 done
echo "End : $(date +"%F_%H-%M-%S")" echo "End : $(date +"%F_%H-%M-%S")"
This diff is collapsed.
...@@ -81,10 +81,10 @@ fi ...@@ -81,10 +81,10 @@ fi
JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}') JAVA=$(grep "javacmd" $CONFIGFILE | awk '{print $2}')
PATHSCRIPT=$(grep "pipelinebase" $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" 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 $GATK -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -o merge.vcf -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE $JAVA -jar /work/gad/shared/bin/GATK_3.8/GenomeAnalysisTK.jar -T CombineVariants -R $REF --variant $INPUTFILE2 --variant $INPUTFILE2 -genotypeMergeOptions UNIQUIFY > $OUTPUTFILE
genotypeMerge_exitcode=$? genotypeMerge_exitcode=$?
echo "GenotypeMerge exit code : $genotypeMerge_exitcode" echo "GenotypeMerge exit code : $genotypeMerge_exitcode"
......
...@@ -3,3 +3,4 @@ pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf ...@@ -3,3 +3,4 @@ pharmagkbase /work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv pharmagktab /work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv
omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv omim /work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM.tsv
header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf header /work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
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