Added IR_database variable in script

joshuakirsch · Mar 27, 2024 · c92f470 · c92f470
1 parent 7fa6681
commit c92f470
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/pseudoR_multiReference_restart.sh b/pseudoR_multiReference_restart.sh
@@ -1,4 +1,4 @@
-while getopts "s:t:d:r:c:m:1:2:3:x:n:h" flag
+while getopts "s:t:d:r:c:m:1:2:3:x:n:i:h" flag
 do
     case "${flag}" in
      s) sraList=${OPTARG};;
@@ -12,6 +12,7 @@ do
    	3) singleton_ending=${OPTARG};;
     x) contig_ending=${OPTARG};;
 	n) sraList_New=${OPTARG};;
+ i) IR_database=${OPTARG};;
 
     esac
 done
@@ -108,4 +109,4 @@ done
 
 bash ${database}/post-analysis_V3.sh -s ../${sraList} -d ${database} 
 Rscript --vanilla ${database}/Final_Output.multiReference.R ../${sraList} final_results/contig_analysis.step1.tsv ${database} contig
-Rscript --vanilla ${database}/Final_Output.multiReference.R ../${sraList} final_results/orf_analysis.step1.tsv ${database} ORF
+Rscript --vanilla ${database}/Final_Output.multiReference.R ../${sraList} final_results/orf_analysis.step1.tsv ${database} ORF