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Anne-Sophie Denommé-Pichon
STR
Commits
3df41650
Commit
3df41650
authored
Feb 16, 2020
by
Anne-Sophie Denommé-Pichon
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Add sample name to SGE job
parent
c7b5da6e
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pipeline.sh
pipeline.sh
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pipeline.sh
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3df41650
...
...
@@ -51,4 +51,4 @@ mkdir -p "$OUTPUTDIR/ehdn"
qsub
-pe
smp 4
-q
batch
-N
"ehdn_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/ehdn/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/ehdn/
$DATE
.log"
wrapper_ehdn.sh
# Delete transfered bam and bai
qsub
-pe
smp 1
-q
batch
-hold_jid
"eh_
$SAMPLE
,tredparse_
$SAMPLE
,gangstr_
$SAMPLE
,ehdn_
$SAMPLE
"
-sync
y
-v
SAMPLE
=
"
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/delete_
$DATE
.log"
wrapper_delete.sh
qsub
-pe
smp 1
-q
batch
-
N
"delete_
$SAMPLE
"
-
hold_jid
"eh_
$SAMPLE
,tredparse_
$SAMPLE
,gangstr_
$SAMPLE
,ehdn_
$SAMPLE
"
-sync
y
-v
SAMPLE
=
"
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/delete_
$DATE
.log"
wrapper_delete.sh
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