refactor: Use settings from make_input_file2.pl

modules/primer3_conf/main.nf

@@ -22,20 +22,30 @@ process primer3_conf {
     ##
     ##
 
+    # The while loop
     echo "SEQUENCE_ID=$(seqkit fx2tab !{target} | cut -f 1)
-    SEQUENCE_TEMPLATE=$(seqkit fx2tab !{target} | cut -f 2)
-    SEQUENCE_TARGET=50000,20
-    SEQUENCE_EXCLUDED_REGION=49965,70
-    PRIMER_TASK=generic
-    PRIMER_PICK_LEFT_PRIMER=1
-    PRIMER_PICK_INTERNAL_OLIGO=0
-    PRIMER_PICK_RIGHT_PRIMER=1
+    TARGET=100,$($len - 200)
+    SEQUENCE=$(seqkit fx2tab !{target} | cut -f 2)
+    PRIMER_PRODUCT_SIZE_RANGE=$($len - 200)-$len
+    # make_input_file2.pl
+    PRIMER_NUM_RETURN=5
     PRIMER_OPT_SIZE=20
     PRIMER_MIN_SIZE=18
-    PRIMER_MAX_SIZE=22
-    PRIMER_PRODUCT_SIZE_RANGE=75-500
-    PRIMER_EXPLAIN_FLAG=1
-    PRIMER_MASK_TEMPLATE=1
+    PRIMER_MAX_SIZE=25
+    PRIMER_OPT_TM=60.0
+    PRIMER_MIN_TM=57.0
+    PRIMER_MAX_TM=63.0
+    PRIMER_MAX_DIFF_TM=2
+    PRIMER_MIN_GC=40.0
+    PRIMER_MAX_GC=60.0
+    PRIMER_MAX_POLY_X=5
+    PRIMER_SALT_CONC=50.0
+    PRIMER_DNA_CONC=50.0
+    PRIMER_NUM_NS_ACCEPTED=0
+    PRIMER_MAX_END_STABILITY=9
+    PRIMER_SELF_ANY=8
+    PRIMER_SELF_END=3
+
     PRIMER_MASK_KMERLIST_PREFIX=!{fasta}
     PRIMER_MASK_KMERLIST_PATH=./kmer_lists/
     =" > !{target.baseName}.primer3.conf