maintien

Master.sh

@@ -52,7 +52,7 @@ fi
 
 
 #Usefull variables
-PIPELINEBASE=`grep pipelinebase $CONFIGFILE | cut -f2`
+PIPELINEBASE=`grep "pipelinebase" $PHARMCONFIG | cut -f2`
 TSVFILE=`grep "pharmagktab" $PHARMCONFIG | cut -f2`
 PHARMGKB=`grep "pharmagkbase" $PHARMCONFIG | cut -f2`
 OMIM=`grep "omim" $PHARMCONFIG | cut -f2`
@@ -81,7 +81,7 @@ 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 $PIPELINEBASE/haplo_scan.sh"
-    qsub -pe smp 1 -N HLAscan_${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 $PIPELINEBASE/haplo_scan.sh
+#    qsub -q batch -pe smp 1 -N HLAscan_${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")"
 
@@ -92,7 +92,7 @@ echo "Start : $(date +"%F_%H-%M-%S")"
 for currentSample in $samples
 do
     echo "Command : qsub -pe smp 1 -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -N varcallSNP_${currentSample} -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.raw.vcf,PHARMGKB=$PHARMGKB,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallSNP.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/annotate_variants_pharmAnnot.sh"
-    qsub -pe smp 1 -N varcallSNP_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.raw.vcf,PHARMGKB=$PHARMGKB,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallSNP.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/annotate_variants_pharmAnnot.sh
+    qsub -q batch -pe smp 1 -N varcallSNP_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.raw.vcf,PHARMGKB=$PHARMGKB,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.pharmacoAnnot.SNP.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallSNP.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/annotate_variants_pharmAnnot.sh
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
@@ -104,7 +104,7 @@ for currentSample in $samples
 do
     cnvfile=`ls -lht $ANALYSISDIR/$currentSample/ | grep "\.annot.tsv" | head -1 | awk '{print $9}'`
     echo "Command : qsub -pe smp 1 -N varcallCNV_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$cnvfile,PHARMGKB=$TSVFILE,OMIM=$OMIM,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallCNV.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_tsv2vcf.sh"
-    qsub -pe smp 1 -N tsv2vcf_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$cnvfile,PHARMGKB=$TSVFILE,OMIM=$OMIM,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallCNV.$logbasenameCNV.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_tsv2vcf.sh
+    qsub -q batch -pe smp 1 -N tsv2vcf_${currentSample} -o $ANALYSISDIR/$currentSample/logs/ -e $ANALYSISDIR/$currentSample/logs/ -v INPUTFILE=$ANALYSISDIR/$currentSample/$cnvfile,PHARMGKB=$TSVFILE,OMIM=$OMIM,REF=$REF,OUTPUTFILE=$ANALYSISDIR/$currentSample/$currentSample.CNV.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/process_varcallCNV.$logbasenameCNV.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/wrapper_tsv2vcf.sh
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
@@ -115,7 +115,7 @@ echo "Start : $(date +"%F_%H-%M-%S")"
 for currentSample in $samples
 do
     echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${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 $PIPELINEBASE/wrapper_create_html.sh
+    qsub -q batch -pe smp 1 -hold_jid varcallCNV_${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")"
 
@@ -126,6 +126,6 @@ echo "Start : $(date +"%F_%H-%M-%S")"
 for currentSample in $samples
 do
     echo "Command : qsub -pe smp 1 -hold_jid varcallCNV_${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.pharmacoAnnot.merge.vcf,LOGFILE=$ANALYSISDIR/$currentSample/logs/merge_file.$logbasename.log,CONFIGFILE=$CONFIGFILE $PIPELINEBASE/merge_GATK.sh
+    qsub -q batch -pe smp 1 -hold_jid varcallCNV_${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
 done
 echo "End : $(date +"%F_%H-%M-%S")"

haplo_scan.sh

@@ -46,14 +46,6 @@ then
     exit 1
 fi
 
-# Check if config file exist
-if [ ! -f $CONFIGFILE ]
-then
-    echo "Config file does not exist"
-    echo "$(date +"%F_%H-%M-%S"): END"
-    touch annotate_variants_snpeff.failed
-    exit 1
-fi
 
 # Check if output file is specified
 if [ -z $SORTIE ]

pharmconfig.tsv

-HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
-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

pharmconfig_epilepsie.tsv

+pipelinebase    /work/gad/shared/pipeline/pharmacogen_test/pharmAnnot
 HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
 pharmagkbase	/work/gad/sv347413/epilepsie/Pipeline/pharmgkb_v2.vcf
 pharmagktab	/work/gad/sv347413/epilepsie/Pipeline/tableau_pharmgkb.tsv

pharmconfig_oncologie.tsv

+pipelinebase	/work/gad/shared/pipeline/pharmacogen_test/pharmAnnot	
 HLAlist	/work/gad/shared/analyse/test_HLA/HLAscan_v1.0/hla-ref-5gene/gene_list
-pharmagkbase	/work/gad/sv347413/epilepsie/Pipeline/pharmgkb_oncologie.vcf
-pharmagktab	/work/gad/sv347413/epilepsie/Pipeline/tableau_oncologie.tsv
-omim	/work/gad/sv347413/epilepsie/Pipeline/tableau_OMIM_oncologie.tsv
+pharmagkbase	/work/gad/sv347413/oncologie/pharmgkb_oncologie_v4.vcf
+pharmagktab	/work/gad/sv347413/oncologie/tableau_oncologie_v2.tsv
+omim	/work/gad/sv347413/oncologie/tableau_OMIM_oncologie.tsv
 header	/work/gad/sv347413/epilepsie/Pipeline/header_CNV.vcf
 reference	/work/gad/shared/pipeline/hg19/index/hg19_essential.fa