Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts

alignment/hisat_genotype.sh

@@ -11,10 +11,9 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:x:y:p:uh opt
+while getopts :x:y:p:uh opt
 do
     case $opt in
-        r) index_path=$OPTARG;;
         x) fq1=$OPTARG;;
         y) fq2=$OPTARG;;
 	u) umi='umi';;
@@ -26,7 +25,7 @@ done
 shift $(($OPTIND -1))
 
 # Check for mandatory options
-if [[ -z $pair_id ]] || [[ -z $index_path ]]; then
+if [[ -z $pair_id ]]; then
     usage
 fi
 
@@ -42,9 +41,9 @@ diff $fq1 $fq2 > difffile
 
 if [ -s difffile ]
 then
-hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
 else
-hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
 fi
 hisatgenotype_locus_samples.py -p 16 --region-list hla.A,hla.B,hla.C,hla.DQA1,hla.DQB1,hla.DRB1,hla.DPB1 --assembly --read-dir hisatgeno_out --out-dir ${pair_id}.hisat_hla > ${pair_id}.hisat_hla.txt
 

variants/svcalling.sh

@@ -11,7 +11,7 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:p:b:i:e:n:a:h opt
+while getopts :r:p:b:i:n:a:h opt
 do
     case $opt in
         r) index_path=$OPTARG;;