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gad-public
pharmAnnot
Commits
3c5a5a82
Commit
3c5a5a82
authored
Aug 07, 2018
by
Simon Verdez
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pipeline works
parent
5f8e477e
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4 changed files
with
19 additions
and
10 deletions
+19
-10
Master.sh
Master.sh
+15
-7
create_html.py
create_html.py
+0
-0
merge_GATK.sh
merge_GATK.sh
+3
-3
pharmconfig.tsv
pharmconfig.tsv
+1
-0
No files found.
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_varcal
l.
$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_varcal
l.
$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_htm
l.
$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_htm
l.
$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.
Click to expand it.
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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