moving the sarscov2 preset from using the refseq Wuhan-1 accession to the more commonly referenced genbank Wuhan-1 accession

Author: nrminor

conf/presets/sarscov2.config

@@ -3,7 +3,7 @@
  *
  * This preset extends the virus preset with SARS-CoV-2 specific settings:
  * - Inherits: Sylph IMG/VR 4.1 database, Panhuman-1 decontamination
- * - Adds: Wuhan-Hu-1 reference sequence (NCBI RefSeq NC_045512.2)
+ * - Adds: Wuhan-Hu-1 reference sequence (GenBank MN908947.3)
  * - Adds: Nextclade SARS-CoV-2 dataset for clade assignment and QC
  *
  * The reference sequence is automatically fetched from NCBI if not provided
@@ -18,10 +18,13 @@
 includeConfig 'virus.config'
 
 params {
-    // SARS-CoV-2 Wuhan-Hu-1 reference sequence (NCBI RefSeq)
-    // Automatically fetched from NCBI Entrez if not a local file
-    refseq  = "NC_045512.2"
-    ref_gbk = "NC_045512.2"
+    // SARS-CoV-2 Wuhan-Hu-1 reference sequence (GenBank)
+    // Using GenBank accession rather than RefSeq (NC_045512.2) because:
+    // - Most primer schemes (ARTIC, QIAseq, etc.) use MN908947.3 coordinates
+    // - Avoids chromosome name mismatches with common primer BED files
+    // - Immutable versioned record ensures reproducibility
+    refseq  = "MN908947.3"
+    ref_gbk = "MN908947.3"
 
     // Nextclade dataset for SARS-CoV-2 clade assignment and phylogenetic QC
     // See available datasets: nextclade dataset list --only-names