Revert "test: Try hard coding the example file?"

This reverts commit 2826ed4.
Functional-Genomics-Lab · Jul 29, 2024 · f21352b · f21352b
1 parent 2826ed4
commit f21352b
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Showing 5 changed files with 18 additions and 19 deletions.
diff --git a/examples/manual.fa b/examples/manual.fa
diff --git a/main.nf b/main.nf
@@ -15,6 +15,6 @@ workflow {
 
   primer3_conf(target,ref)
   primer3_index(ref)
-  primer3_calc(primer3_conf.out)
+  primer3_calc(primer3_conf.out,primer3_index.out)
   primer3_results2fasta(primer3_calc.out)
 }
diff --git a/modules/primer3_calc/main.nf b/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"

diff --git a/modules/primer3_conf/main.nf b/modules/primer3_conf/main.nf
@@ -5,7 +5,7 @@ process primer3_conf {
 
     input:
     path target
-    path fasta // TODO Cut this out
+    path fasta
 
     output:
     path "custom_primer3.conf"
@@ -23,21 +23,22 @@ process primer3_conf {
     ##
     ##
 
-    echo "SEQUENCE_ID=example
-    SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
-    SEQUENCE_TARGET=37,21
+    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=1
+    PRIMER_PICK_INTERNAL_OLIGO=0
     PRIMER_PICK_RIGHT_PRIMER=1
-    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_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_MASK_KMERLIST_PREFIX=!{fasta}
+    PRIMER_MASK_KMERLIST_PATH=./kmer_lists/
     =" > custom_primer3.conf
     '''
 }
diff --git a/nextflow.config b/nextflow.config
@@ -7,10 +7,10 @@ docker.enabled = true
 wave.enabled = true
 
 profiles {
-    example {
+    test {
         params {
-            fasta = "${projectDir}/examples/manual.fa"
-            targetseq = "GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG"
+            fasta = "${projectDir}/examples/example.fa"
+            targetseq = "ATGGGAGGAGAAGGGTATCGCGG"
         }
     }
 }