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Commit 3df41650 authored by Anne-Sophie Denommé-Pichon's avatar Anne-Sophie Denommé-Pichon
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Add sample name to SGE job

parent c7b5da6e
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pipeline.sh
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...@@ -51,4 +51,4 @@ mkdir -p "$OUTPUTDIR/ehdn" ...@@ -51,4 +51,4 @@ mkdir -p "$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/$DATE.log" wrapper_ehdn.sh qsub -pe smp 4 -q batch -N "ehdn_$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 # 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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