test: Try hard coding the example file?

Had to remove the kmer lists as well

examples/manual.fa

@@ -0,0 +1,2 @@
+>example
+GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG

main.nf

@@ -15,6 +15,6 @@ workflow {
 
   primer3_conf(target,ref)
   primer3_index(ref)
-  primer3_calc(primer3_conf.out,primer3_index.out)
+  primer3_calc(primer3_conf.out)
   primer3_results2fasta(primer3_calc.out)
 }

modules/primer3_calc/main.nf

@@ -6,7 +6,7 @@ process primer3_calc {
 
     input:
     path conf
-    path kmer_lists, stageAs: 'kmer_lists/*'
+    // path kmer_lists, stageAs: 'kmer_lists/*'
 
     output:
     path "*primer3.txt"

modules/primer3_conf/main.nf

@@ -5,7 +5,7 @@ process primer3_conf {
 
     input:
     path target
-    path fasta
+    path fasta // TODO Cut this out
 
     output:
     path "custom_primer3.conf"
@@ -23,22 +23,21 @@ process primer3_conf {
     ##
     ##
 
-    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
+    echo "SEQUENCE_ID=example
+    SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
+    SEQUENCE_TARGET=37,21
     PRIMER_TASK=generic
     PRIMER_PICK_LEFT_PRIMER=1
-    PRIMER_PICK_INTERNAL_OLIGO=0
+    PRIMER_PICK_INTERNAL_OLIGO=1
     PRIMER_PICK_RIGHT_PRIMER=1
-    PRIMER_OPT_SIZE=20
-    PRIMER_MIN_SIZE=18
-    PRIMER_MAX_SIZE=22
-    PRIMER_PRODUCT_SIZE_RANGE=75-500
+    PRIMER_OPT_SIZE=18
+    PRIMER_MIN_SIZE=15
+    PRIMER_MAX_SIZE=21
+    PRIMER_MAX_NS_ACCEPTED=1
+    PRIMER_PRODUCT_SIZE_RANGE=75-100
+    P3_FILE_FLAG=1
+    SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
     PRIMER_EXPLAIN_FLAG=1
-    PRIMER_MASK_TEMPLATE=1
-    PRIMER_MASK_KMERLIST_PREFIX=!{fasta}
-    PRIMER_MASK_KMERLIST_PATH=./kmer_lists/
     =" > custom_primer3.conf
     '''
 }

nextflow.config

@@ -7,10 +7,10 @@ docker.enabled = true
 wave.enabled = true
 
 profiles {
-    test {
+    example {
         params {
-            fasta = "${projectDir}/examples/example.fa"
-            targetseq = "ATGGGAGGAGAAGGGTATCGCGG"
+            fasta = "${projectDir}/examples/manual.fa"
+            targetseq = "GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG"
         }
     }
 }