diff --git a/.github/data/reads_to_simulate.csv b/.github/data/reads_to_simulate.csv
index 1ceaef9..a39da26 100644
--- a/.github/data/reads_to_simulate.csv
+++ b/.github/data/reads_to_simulate.csv
@@ -1 +1 @@
-NC002973.6,.github/data/assemblies/NC_002973.6.fa
+NC_000962.3,.github/data/refs/NC_000962.3.fa
diff --git a/.github/scripts/download_assemblies.sh b/.github/scripts/download_assemblies.sh
deleted file mode 100755
index 12692b0..0000000
--- a/.github/scripts/download_assemblies.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-mkdir -p .github/data/assemblies
-
-curl -o .github/data/assemblies/NC_002973.6.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_002973.6&db=nucleotide&rettype=fasta"
diff --git a/.github/scripts/download_refs.sh b/.github/scripts/download_refs.sh
new file mode 100755
index 0000000..4427fca
--- /dev/null
+++ b/.github/scripts/download_refs.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+mkdir -p .github/data/refs
+
+curl -o .github/data/refs/NC_000962.3.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_000962.3&db=nucleotide&rettype=fasta"
+curl -o .github/data/refs/NC_002973.6.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_002973.6&db=nucleotide&rettype=fasta"
diff --git a/.github/scripts/run_pipeline.sh b/.github/scripts/run_pipeline.sh
index 0038f00..629f296 100755
--- a/.github/scripts/run_pipeline.sh
+++ b/.github/scripts/run_pipeline.sh
@@ -15,6 +15,6 @@ nextflow run main.nf \
 	 --fastq_input .github/data/fastq \
 	 --outdir .github/data/test_output \
 	 --min_depth 5 \
-	 --ref .github/data/refs/NC_045512.2.fasta \
+	 --ref .github/data/refs/NC_000962.3.fa \
 	 -with-report .github/data/test_output/nextflow_report.html \
  	 -with-trace .github/data/test_output/nextflow_trace.tsv