diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a4ae5436..404eeb4a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -69,6 +69,7 @@ jobs:
           - "--spades_mode metaviral"
           - "--skip_plasmidid false --skip_asciigenome"
           - "--additional_annotation ./GCA_009858895.3_ASM985889v3_genomic.gtf.gz"
+          - "--bowtie2_index ./GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -92,6 +93,11 @@ jobs:
         run: |
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz
 
+      - name: Download prebuild bowtie2 index
+        if: contains(matrix.parameters, 'bowtie2_index')
+        run: |
+          wget https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.bt2.index.tar.gz
+
       - name: Run pipeline with various parameters
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --publish_dir_mode link --outdir ./results
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8c05c8c5..cc3fda4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #417](https://github.com/nf-core/viralrecon/pull/417)] - Allow skipping of Freyja bootstrapping module & freyja module update
 - [[PR #434](https://github.com/nf-core/viralrecon/pull/434)] - Add blast result filtering through `min_contig_length` and `min_perc_contig_aligned`.
 - [[PR #438](https://github.com/nf-core/viralrecon/pull/438)] - Update fastp container to 0.23.4
+- [[PR #439](https://github.com/nf-core/viralrecon/pull/439)] - Fix cardinality issue when using `--bowtie2_index`
 
 ### Parameters
 
diff --git a/subworkflows/local/prepare_genome_illumina.nf b/subworkflows/local/prepare_genome_illumina.nf
index 27768726..efc79b39 100644
--- a/subworkflows/local/prepare_genome_illumina.nf
+++ b/subworkflows/local/prepare_genome_illumina.nf
@@ -158,12 +158,12 @@ workflow PREPARE_GENOME {
         if (bowtie2_index) {
             if (bowtie2_index.endsWith('.tar.gz')) {
                 UNTAR_BOWTIE2_INDEX (
-                    [ [:], bowtie2_index ]
+                    [ [:], file(bowtie2_index) ]
                 )
-                ch_bowtie2_index = UNTAR_BOWTIE2_INDEX.out.untar.map { it[1] }
+                ch_bowtie2_index = UNTAR_BOWTIE2_INDEX.out.untar
                 ch_versions      = ch_versions.mix(UNTAR_BOWTIE2_INDEX.out.versions)
             } else {
-                ch_bowtie2_index = Channel.value(file(bowtie2_index))
+                ch_bowtie2_index = [ [:], file(bowtie2_index) ]
             }
         } else {
             BOWTIE2_BUILD (
@@ -246,7 +246,7 @@ workflow PREPARE_GENOME {
     gff                  = ch_gff                  // path: genome.gff
     fai                  = ch_fai                  // path: genome.fai
     chrom_sizes          = ch_chrom_sizes          // path: genome.sizes
-    bowtie2_index        = ch_bowtie2_index        // path: bowtie2/index/
+    bowtie2_index        = ch_bowtie2_index        // channel: [ [:], bowtie2/index/ ]
     primer_bed           = ch_primer_bed           // path: primer.bed
     primer_collapsed_bed = ch_primer_collapsed_bed // path: primer.collapsed.bed
     primer_fasta         = ch_primer_fasta         // path: primer.fasta