From f21352ba596f83b1ac410f18bd01e5980ce2ddbe Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Mon, 29 Jul 2024 14:46:31 -0500
Subject: [PATCH] Revert "test: Try hard coding the example file?"

This reverts commit 2826ed4d16d867bdc2705752a4e8a29ffb80d144.
---
 examples/manual.fa           |  2 --
 main.nf                      |  2 +-
 modules/primer3_calc/main.nf |  2 +-
 modules/primer3_conf/main.nf | 25 +++++++++++++------------
 nextflow.config              |  6 +++---
 5 files changed, 18 insertions(+), 19 deletions(-)
 delete mode 100644 examples/manual.fa

diff --git a/examples/manual.fa b/examples/manual.fa
deleted file mode 100644
index e866202..0000000
--- a/examples/manual.fa
+++ /dev/null
@@ -1,2 +0,0 @@
->example
-GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
diff --git a/main.nf b/main.nf
index 6168934..93869d4 100644
--- 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
index 4bb5e31..6f08c88 100644
--- 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
index 14fa9e8..485b300 100644
--- 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
index 18728bf..55f8946 100644
--- 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"
         }
     }
 }