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Commit 85802bc1 authored by Anne-Sophie Denommé-Pichon's avatar Anne-Sophie Denommé-Pichon
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Update queue and add stretch wrapper

parent 5b438991
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Showing with 55 additions and 18 deletions
launch_expansionhunter.sh
View file @ 85802bc1
...@@ -11,10 +11,10 @@ ...@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102 ## Creation Date : 20191102
## last revision date : 20191102 ## last revision date : 20191126
## Known bugs : None ## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/ExpansionHunter/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
...@@ -27,5 +27,5 @@ then ...@@ -27,5 +27,5 @@ then
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_expansionhunter.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_expansionhunter.sh
fi fi
launch_gangstr.sh
View file @ 85802bc1
...@@ -11,21 +11,23 @@ ...@@ -11,21 +11,23 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104 ## Creation Date : 20191104
## last revision date : 20191117 ## last revision date : 20191126
## Known bugs : None ## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/GangSTR/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log" LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
INSERTMEAN="359.4"
INSERTDEV="80.1204"
# Launch the script on local host with --local option and on SGE with qsub without the --local option # Launch the script on local host with --local option and on SGE with qsub without the --local option
if [ $# -eq 1 ] && [ "x$1" = x--local ] if [ $# -eq 1 ] && [ "x$1" = x--local ]
then then
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_gangstr.sh" INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" INSERTMEAN="$INSERTMEAN" INSERTDEV="$INSERTDEV" "$(dirname "$0")/wrapper_gangstr.sh"
else else
mkdir -p "$OUTPUTDIR" mkdir -p "$OUTPUTDIR"
qsub -pe smp 1 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_gangstr.sh qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE",INSERTMEAN="$INSERTMEAN",INSERTDEV="$INSERTDEV" wrapper_gangstr.sh
fi fi
launch_lobstr.sh
View file @ 85802bc1
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
## last revision date : 20191104 ## last revision date : 20191104
## Known bugs : None ## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18/dijen017.sorted.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/LobSTR/$DATE"
OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE" OUTPUTPREFIX="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE"
......
launch_stretch.sh 0 → 100755
View file @ 85802bc1
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_stretch.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing STRetch script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191118
## last revision date : 20191127
## Known bugs : None
# INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/shortdijen017/dijen017.short.bam
DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/STRetch/$DATE"
LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
# Launch the script on local host with --local option and on SGE with qsub without the --local option
if [ $# -eq 1 ] && [ "x$1" = x--local ]
then
mkdir -p "$OUTPUTDIR"
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTDIR" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_stretch.sh"
else
mkdir -p "$OUTPUTDIR"
qsub -pe smp 16 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR",LOGFILE="$LOGFILE" wrapper_stretch.sh
fi
launch_tredparse.sh
View file @ 85802bc1
...@@ -11,10 +11,10 @@ ...@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191103 ## Creation Date : 20191103
## last revision date : 20191103 ## last revision date : 20191126
## Known bugs : None ## Known bugs : None
INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
DATE="$(date +"%F_%H-%M-%S")" DATE="$(date +"%F_%H-%M-%S")"
OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE" OUTPUTDIR="/work/gad/shared/analyse/STR/Tredparse/$DATE"
LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log" LOGFILE="$OUTPUTDIR/$(basename "$INPUTFILE")_$DATE.log"
......
wrapper_gangstr.sh
View file @ 85802bc1
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr ## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104 ## Creation Date : 20191104
## last revision date : 20191104 ## last revision date : 20191127
## Known bugs : None ## Known bugs : None
...@@ -50,14 +50,19 @@ echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \ ...@@ -50,14 +50,19 @@ echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \ --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \ --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
--out "$OUTPUTPREFIX" \ --out "$OUTPUTPREFIX" \
--verbose" --verbose \
--insertmean "$INSERTMEAN" \
--insertsdev "$INSERTDEV""
/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \ /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
--bam "$INPUTFILE" \ --bam "$INPUTFILE" \
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \ --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \ --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
--out "$OUTPUTPREFIX" \ --out "$OUTPUTPREFIX" \
--verbose --verbose \
--insertmean "$INSERTMEAN" \
--insertsdev "$INSERTDEV"
gangstr_exitcode=$? gangstr_exitcode=$?
......
wrapper_samtoolssortbyread.sh
View file @ 85802bc1
#! /bin/sh #! /bin/sh
samtools sort -n -@64 -T /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18 -o /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam samtools sort -n -@64 --check=quiet -T sortbyread /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26 -o /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam
wrapper_stretch.sh
View file @ 85802bc1
...@@ -47,15 +47,13 @@ fi ...@@ -47,15 +47,13 @@ fi
# Launch script command and check exit code # Launch script command and check exit code
echo "cd "$OUTPUTDIR" echo "cd "$OUTPUTDIR"
/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \ /work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
run -p \ run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
/work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \ /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
"$INPUTFILE"" "$INPUTFILE""
cd "$OUTPUTDIR" cd "$OUTPUTDIR"
/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \ /work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe \
run -p run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed \
/work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \ /work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy \
"$INPUTFILE" "$INPUTFILE"
......
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