HyPhy v0.2: replace CDS input with genome FASTA + GTF

workflows/comparative_genomics/hyphy/CHANGELOG.md

@@ -1,5 +1,16 @@
 # Changelog
 
+## [0.2] - 2026-07-02
+
+### Changed
+- Replaced single `reference cds` input with `reference GTF` + `reference Fasta` inputs across all HyPhy workflows
+  - Enables automated CDS extraction from annotated reference genomes
+  - Aligns workflow parameters with BRC Analytics `ASSEMBLY_FASTA_URL` and `GENE_MODEL_URL` variables
+- Updated CAPHEINE, HyPhy Core, HyPhy Compare, and HyPhy Preprocessing to version 0.2
+- Replaced `denv1_ref_cds.fasta` with `denv1_genome.fasta` (NC_001477.1 full genome) as the reference FASTA test input
+- Added `denv1_ref.gtf` with coordinates for two DENV1 CDS regions (capsid protein C and prM)
+- Updated test parameter files to use genome FASTA + GTF inputs
+
 ## [0.1] - 2026-02-26
 
 ### Added

workflows/comparative_genomics/hyphy/README.md

@@ -11,7 +11,8 @@ This directory contains Galaxy workflows for running HyPhy (Hypothesis Testing u
 The main workflow that orchestrates the complete HyPhy pipeline, including codon-aware preprocessing and optional branch-comparison analyses. Inspired by the [veg/capheine](https://github.com/veg/capheine) Nextflow implementation, version 1.1.0.
 
 **Inputs:**
-- **Reference CDS FASTA** (required): Multi-gene CDS reference file (e.g., from NCBI)
+- **Reference GTF** (required): GTF annotation for the reference genome
+- **Reference Fasta** (required): Genome FASTA for the reference assembly
 - **Unaligned sequences** (required): List collection of FASTA files, one per sample
 - **Foreground regexp** (optional): Regular expression to match foreground sequence names for branch labeling
 - **Foreground list** (optional): Dataset with cleaned sequence identifiers for foreground branches
@@ -52,14 +53,16 @@ Subworkflow for sequence cleanup and codon-aware alignment.
 ## Test Data
 
 The `test-data/` directory contains:
-- `denv1_ref_cds.fasta`: Reference coding sequences from Dengue virus 1
-- `foreground_seqs_list.tabular`: Example foreground sequence identifiers
+- `denv1_genome.fasta`: Reference genome FASTA for Dengue virus 1 (NC_001477.1)
+- `denv1_ref.gtf`: GTF annotation for two DENV1 CDS regions (capsid protein C and prM; coords 95–394 and 437–934)
+- `denv1_ref_cds.fasta`: Pre-extracted CDS sequences (retained for reference; not used as a workflow input in v0.2+)
+- `foreground_seqs_list.txt`: Example foreground sequence identifiers
 - `unaligned_seqs/`: Directory with 39 unaligned FASTA files for testing
 
 ## Running Tests
 
 Tests are defined in `capheine-core-and-compare-tests.yml` with four scenarios:
-1. Core only (reference CDS + unaligned sequences)
+1. Core only (reference GTF + reference Fasta + unaligned sequences)
 2. Core + Compare with regex (no foreground list)
 3. Core + Compare with foreground list (no regex)
 4. Core + Compare with all inputs (regex takes precedence)

workflows/comparative_genomics/hyphy/capheine-core-and-compare-tests.yml

@@ -1,8 +1,12 @@
 - doc: Test CAPHEINE with reference CDS and unaligned sequences only (Core workflow only)
   job:
-    reference cds:
+    reference GTF:
       class: File
-      path: test-data/denv1_ref_cds.fasta
+      path: test-data/denv1_ref.gtf
+      filetype: gtf
+    reference Fasta:
+      class: File
+      path: test-data/denv1_genome.fasta
       filetype: fasta
     unaligned sequences:
       class: Collection
@@ -46,9 +50,13 @@
 
 - doc: Test CAPHEINE with reference CDS, unaligned sequences, and regex (no foreground list)
   job:
-    reference cds:
+    reference GTF:
+      class: File
+      path: test-data/denv1_ref.gtf
+      filetype: gtf
+    reference Fasta:
       class: File
-      path: test-data/denv1_ref_cds.fasta
+      path: test-data/denv1_genome.fasta
       filetype: fasta
     unaligned sequences:
       class: Collection
@@ -105,9 +113,13 @@
 
 - doc: Test CAPHEINE with reference CDS, unaligned sequences, and foreground list (no regex)
   job:
-    reference cds:
+    reference GTF:
       class: File
-      path: test-data/denv1_ref_cds.fasta
+      path: test-data/denv1_ref.gtf
+      filetype: gtf
+    reference Fasta:
+      class: File
+      path: test-data/denv1_genome.fasta
       filetype: fasta
     unaligned sequences:
       class: Collection
@@ -168,9 +180,13 @@
 
 - doc: Test CAPHEINE with all inputs (reference CDS, unaligned sequences, regex, and foreground list)
   job:
-    reference cds:
+    reference GTF:
+      class: File
+      path: test-data/denv1_ref.gtf
+      filetype: gtf
+    reference Fasta:
       class: File
-      path: test-data/denv1_ref_cds.fasta
+      path: test-data/denv1_genome.fasta
       filetype: fasta
     unaligned sequences:
       class: Collection

workflows/comparative_genomics/hyphy/hyphy-compare.ga

@@ -381,5 +381,5 @@
     "tags": [],
     "uuid": "9357601d-c7cf-4341-bf87-a5b0fca7e57b",
     "version": 1,
-    "release": "0.1"
+    "release": "0.2"
 }

workflows/comparative_genomics/hyphy/hyphy-core-tests.yml

@@ -1,8 +1,12 @@
 - doc: Test HyPhy Core produces HyPhy JSON collections
   job:
-    reference cds:
+    reference GTF:
       class: File
-      path: test-data/denv1_ref_cds.fasta
+      path: test-data/denv1_ref.gtf
+      filetype: gtf
+    reference Fasta:
+      class: File
+      path: test-data/denv1_genome.fasta
       filetype: fasta
     unaligned sequences:
       class: Collection
@@ -31,41 +35,41 @@
   outputs:
     meme_output:
       element_tests:
-        "NC_001477.1|capsid_protein_C|95-394_DENV1":
+        "capsid_protein_C":
           asserts:
             has_text:
               text: "{"
-        "NC_001477.1|membrane_glycoprotein":
+        "membrane_glycoprotein_precursor_prM":
           asserts:
             has_text:
               text: "{"
     prime_output:
       element_tests:
-        "NC_001477.1|capsid_protein_C|95-394_DENV1":
+        "capsid_protein_C":
           asserts:
             has_text:
               text: "{"
-        "NC_001477.1|membrane_glycoprotein":
+        "membrane_glycoprotein_precursor_prM":
           asserts:
             has_text:
               text: "{"
     busted_output:
       element_tests:
-        "NC_001477.1|capsid_protein_C|95-394_DENV1":
+        "capsid_protein_C":
           asserts:
             has_text:
               text: "{"
-        "NC_001477.1|membrane_glycoprotein":
+        "membrane_glycoprotein_precursor_prM":
           asserts:
             has_text:
               text: "{"
     fel_output:
       element_tests:
-        "NC_001477.1|capsid_protein_C|95-394_DENV1":
+        "capsid_protein_C":
           asserts:
             has_text:
               text: "{"
-        "NC_001477.1|membrane_glycoprotein":
+        "membrane_glycoprotein_precursor_prM":
           asserts:
             has_text:
               text: "{"