diff --git a/README.md b/README.md
index 3ebe621..0220c5d 100644
--- a/README.md
+++ b/README.md
@@ -16,10 +16,10 @@ This is included in the `data` folder. Just run `get_clair3_models.sh` to downlo
 Can run with bcftools or with clair3
 ```bash
 nextflow run . --workflow bcftools --input_dir test_data/assemblers --publish_dir results \
-	--ref-fasta data/h37rv_20231215.fa.gz
+	--ref-fasta data/NC_000962.3.fa.gz
 
 nextflow run . --workflow clair3 --input_dir test_data/assemblers --publish_dir results \
-	--ref-fasta data/h37rv_20231215.fa.gz --clair3_models_dir data/clair3_models \
+	--ref-fasta data/NC_000962.3.fa.gz --clair3_models_dir data/clair3_models \
   --basecalling_model dna_r10.4.1_e8.2_400bps_sup@v4.3.0
 ```
 
diff --git a/data/h37rv_20231215.fa.gz b/data/NC_000962.3.fa.gz
similarity index 100%
rename from data/h37rv_20231215.fa.gz
rename to data/NC_000962.3.fa.gz
diff --git a/data/h37rv_20231215.fa.gz.fai b/data/NC_000962.3.fa.gz.fai
similarity index 100%
rename from data/h37rv_20231215.fa.gz.fai
rename to data/NC_000962.3.fa.gz.fai
diff --git a/main.nf b/main.nf
index f5452c3..fa4eefb 100644
--- a/main.nf
+++ b/main.nf
@@ -26,22 +26,32 @@ workflow {
         exit(0)
     }
 
-    input_files = Channel.fromPath("${params.input_dir}/${params.input_single_suffix}", checkIfExists: true)
+    input_files = Channel
+        .fromPath("${params.input_dir}/${params.input_single_suffix}", checkIfExists: true)
         .ifEmpty { error("cannot find any reads matching ${params.input_single_suffix} in ${params.input_dir}") }
         .map { it -> tuple(it.getName().replaceFirst(/(?i)\.(fastq|fq)\.gz$/, ""), it) }
 
     input_files.take(3).view()
 
-    ref = Channel.fromPath("${params.ref_fasta}").first()
+    read_ch = input_files.map { it ->
+        [
+            it[0],
+            it[1],
+            file(params.ref_fasta),
+            params.reference,
+            params.accession,
+        ]
+    }
+
     clair3_models_dir = params.clair3_models_dir.startsWith("/")
         ? params.clair3_models_dir
         : "${projectDir}/${params.clair3_models_dir}"
 
     if (params.workflow == "clair3") {
-        rundial(input_files, ref, clair3_models_dir, params.basecalling_model)
+        rundial(read_ch, clair3_models_dir, params.basecalling_model)
     }
     else if (params.workflow == "bcftools") {
-        rundial_with_bcftools(input_files, ref)
+        rundial_with_bcftools(read_ch)
     }
     else {
         error("Please provide a valid workflow: bcftools or clair3")
@@ -52,74 +62,83 @@ workflow {
 workflow rundial {
     take:
     fastq_files
-    ref
     clair3_models_dir
     dorado_model
 
     main:
+
+    ref_name_ch = fastq_files.map { it -> [it[0], it[2]] }
+
+    ref_path_ch = fastq_files.map { it -> [it[0], it[4]] }
+
+    fastq_files = fastq_files.map { it -> tuple(it[0], it[1], it[4]) }
+
     clair3_model = get_clair3_model(dorado_model)
 
     valid_model_ch = fastq_files
         .combine(clair3_model)
-        .filter { it -> it[2] != "failed" }
-        .map { it -> tuple(it[0], it[1]) }
+        .filter { it -> it[3] != "failed" }
+        .map { it -> tuple(it[0], it[1], it[2]) }
     invalid_model_ch = fastq_files
         .combine(clair3_model)
-        .filter { it -> it[2] == "failed" }
-        .map { it -> tuple(it[0], it[1]) }
+        .filter { it -> it[3] == "failed" }
+        .map { it -> tuple(it[0], it[1], it[2]) }
 
     valid_model_ch.take(1).view { "Appropriate Clair3 Model Found" }
     invalid_model_ch.take(1).view { "No appropriate Clair3 Model Found" }
 
     // If no appropriate clair3 model is found, use bcftools
-    rundial_with_bcftools(invalid_model_ch, ref)
+    rundial_with_bcftools(invalid_model_ch)
 
     // If appropriate clair3 model is found, run clair3
     model_path = clair3_model.map { it -> clair3_models_dir + "/${it}.tar.gz" }
     model_path.view { "Using Clair3 Model: ${it}" }
 
-    minimap2(valid_model_ch, ref)
-    clair3(minimap2.out.sorted_alignment, ref, model_path)
+    minimap2(valid_model_ch)
+    clair3(minimap2.out.sorted_alignment, model_path)
 
     clair3_filter_params = Channel.fromPath("${moduleDir}/process/clair3_filter_params.yml").first()
     apply_filters_clair3(clair3.out.vcf, clair3_filter_params, "clair3_")
 
     // Still use normal params with bcftools support vcf
     filter_params = Channel.fromPath("${moduleDir}/process/filter_params.yml").first()
-    call_snps(minimap2.out.sorted_alignment, ref)
+    call_snps(minimap2.out.sorted_alignment)
     apply_filters(call_snps.out.gvcf, filter_params, "bcftools_")
 
 
     consensus_params = Channel.fromPath("${moduleDir}/process/clair3_consensus_params.yml").first()
     calls = apply_filters.out.filtered_gvcf.join(apply_filters_clair3.out.filtered_gvcf)
-    make_clair3_consensus(calls, ref, consensus_params)
+                                           .join(ref_path_ch) 
+    calls.view { "Calls channel: ${it}" }
+    make_clair3_consensus(calls, consensus_params)
 
     emit:
-    alignment = rundial_with_bcftools.out.alignment.concat(minimap2.out.sorted_alignment)
-    gvcf = rundial_with_bcftools.out.gvcf.concat(clair3.out.vcf)
-    final_fasta = rundial_with_bcftools.out.final_fasta.concat(make_clair3_consensus.out.final_fasta)
-    variable_length_fasta = rundial_with_bcftools.out.variable_length_fasta.concat(make_clair3_consensus.out.variable_length_fasta)
-    final_vcf = rundial_with_bcftools.out.final_vcf.concat(make_clair3_consensus.out.final_vcf)
-    full_vcf = rundial_with_bcftools.out.full_vcf.concat(make_clair3_consensus.out.full_vcf)
-    creation_report_json = rundial_with_bcftools.out.creation_report_json.concat(make_clair3_consensus.out.report_json)
+    alignment = rundial_with_bcftools.out.alignment.concat(minimap2.out.sorted_alignment).join(ref_name_ch).map { it -> tuple(it[0], it[1], it[3], null, it[2]) }
+    gvcf = rundial_with_bcftools.out.gvcf.concat(clair3.out.vcf).join(ref_name_ch)
+    final_fasta = rundial_with_bcftools.out.final_fasta.concat(make_clair3_consensus.out.final_fasta).join(ref_name_ch)
+    variable_length_fasta = rundial_with_bcftools.out.variable_length_fasta.concat(make_clair3_consensus.out.variable_length_fasta).join(ref_name_ch)
+    final_vcf = rundial_with_bcftools.out.final_vcf.concat(make_clair3_consensus.out.final_vcf).join(ref_name_ch)
+    full_vcf = rundial_with_bcftools.out.full_vcf.concat(make_clair3_consensus.out.full_vcf).join(ref_name_ch)
+    creation_report_json = rundial_with_bcftools.out.creation_report_json.concat(make_clair3_consensus.out.report_json).join(ref_name_ch)
 }
 
 
 workflow rundial_with_bcftools {
     take:
     fastq_files
-    ref
 
     main:
     filter_params = Channel.fromPath("${moduleDir}/process/filter_params.yml").first()
     consensus_params = Channel.fromPath("${moduleDir}/process/consensus_params.yml").first()
 
-    minimap2(fastq_files, ref)
-    call_all(minimap2.out.sorted_alignment, ref)
+    minimap2(fastq_files)
+    call_all(minimap2.out.sorted_alignment)
     apply_filters(call_all.out.gvcf, filter_params, "")
 
     calls = apply_filters.out.filtered_gvcf
-    make_consensus(calls, ref, consensus_params)
+    calls = calls.join(fastq_files).map { it -> tuple(it[0], it[1], it[3]) }
+    calls.view { "Calls channel: ${it}" }
+    make_consensus(calls, consensus_params)
 
     emit:
     alignment = minimap2.out.sorted_alignment
diff --git a/nextflow.config b/nextflow.config
index d59805b..d10e86b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,9 +10,13 @@ params {
     help = ''
     input_dir = ''
     workflow = 'clair3'
-    ref_fasta = 'data/h37rv_20231215.fa.gz'
+    ref_fasta = 'data/NC_000962.3.fa.gz'
     clair3_models_dir = 'data/clair3_models'
     basecalling_model = '' // e.g. "dna_r9.4.1_450bps_sup_prom"
+    reference_genome_suffix = '.fa.gz'
+    reference_genomes_dir = 'test_data/ref_data/'            
+    accession = 'NC_000962.3'
+    reference = 'Mycobacterium tuberculosis'
 }
 
 profiles {
diff --git a/process/consensus.nf b/process/consensus.nf
index ee8e01f..ca7e756 100644
--- a/process/consensus.nf
+++ b/process/consensus.nf
@@ -36,8 +36,7 @@ process make_consensus {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path(filtered_gvcf)
-    path reference
+    tuple val(sample_name), path(filtered_gvcf), path(reference)
     path consensus_params
 
     output:
@@ -76,8 +75,7 @@ process make_clair3_consensus {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path("filtered.gvcf.gz"), path("clair3.vcf.gz")
-    path reference
+    tuple val(sample_name), path("filtered.gvcf.gz"), path("clair3.vcf.gz"), path(reference)
     path consensus_params
 
     output:
diff --git a/process/variant_calling.nf b/process/variant_calling.nf
index 5899f4d..de8d317 100644
--- a/process/variant_calling.nf
+++ b/process/variant_calling.nf
@@ -14,11 +14,10 @@ process minimap2 {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path(fq)
-    path reference
+    tuple val(sample_name), path(fq), path(reference)
 
     output:
-    tuple val(sample_name), path("final.bam"), emit: sorted_alignment
+    tuple val(sample_name), path("final.bam"), path(reference), emit: sorted_alignment
 
     script:
     """
@@ -43,8 +42,7 @@ process call_snps {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path(sorted_alignment)
-    path reference
+    tuple val(sample_name), path(sorted_alignment), path(reference)
 
     output:
     tuple val(sample_name), path("calls.gvcf.gz"), emit: gvcf
@@ -89,8 +87,7 @@ process call_all {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path(sorted_alignment)
-    path reference
+    tuple val(sample_name), path(sorted_alignment), path(reference)
 
     output:
     tuple val(sample_name), path("calls.gvcf.gz"), emit: gvcf
@@ -99,8 +96,10 @@ process call_all {
     """
     echo "Running bcftools mpileup in parallel"
 
+    gunzip -c ${reference} > ref.fasta # Handle gzipped (but not bgzipped) reference input
+
     # script also makes indexes
-    multithreaded_bcftools -a ${sorted_alignment} -r ${reference} \
+    multithreaded_bcftools -a ${sorted_alignment} -r ref.fasta \
         -o pileup.bcf -t ${task.cpus} \
         --settings "-x -Q 10 -a INFO/SCR,INFO/ADR,INFO/ADF,FORMAT/SP,FORMAT/AD -h100 -M10000"
 
@@ -109,10 +108,10 @@ process call_all {
     # Report all alleles during calling
     bcftools call --threads ${task.cpus} --ploidy 1 -m -A -V indels pileup.bcf \
         | bcftools filter -e 'DP==0' \
-        | bcftools norm -d exact -f ${reference} -Oz -o snps.gvcf.gz
+        | bcftools norm -d exact -f ref.fasta -Oz -o snps.gvcf.gz
     bcftools call --threads ${task.cpus} --ploidy 1 -m -A -v -V snps pileup.bcf \
         | bcftools filter -e 'DP==0' \
-        | bcftools norm -d exact -f ${reference} -Oz -o indels.gvcf.gz
+        | bcftools norm -d exact -f ref.fasta -Oz -o indels.gvcf.gz
     bcftools index snps.gvcf.gz
     bcftools index indels.gvcf.gz
     bcftools concat -a snps.gvcf.gz indels.gvcf.gz -o calls.gvcf
@@ -166,8 +165,7 @@ process clair3 {
     pod label: "run_id", value: "${params.run_id}"
 
     input:
-    tuple val(sample_name), path(bam)
-    path reference
+    tuple val(sample_name), path(bam), path(reference)
     path model
 
     output:
diff --git a/test_data/clair3_consensus/clair3.vcf b/test_data/clair3_consensus/clair3.vcf
index c4399f8..d80b2cc 100644
--- a/test_data/clair3_consensus/clair3.vcf
+++ b/test_data/clair3_consensus/clair3.vcf
@@ -1,8 +1,8 @@
 ##fileformat=VCFv4.2
 ##source=Clair3
 ##clair3_version=1.0.4
-##cmdline=/home/ubuntu/miniconda3/envs/clair3/bin/run_clair3.sh --bam_fn=/home/ubuntu/pipelines/sundial/MHall_comparison/assembly/ont/4.sorted.bam --ref_fn=/home/ubuntu/pipelines/sundial/data/h37rv_20231215.fa.gz --threads=8 --platform=ont --model_path=/home/ubuntu/miniconda3/envs/clair3/bin/models/r941_prom_sup_g5014 --include_all_ctgs --print_ref_calls --gvcf --no_phasing_for_fa --output=clair_out/4
-##reference=/home/ubuntu/pipelines/sundial/data/h37rv_20231215.fa.gz
+##cmdline=/home/ubuntu/miniconda3/envs/clair3/bin/run_clair3.sh --bam_fn=/home/ubuntu/pipelines/sundial/MHall_comparison/assembly/ont/4.sorted.bam --ref_fn=/home/ubuntu/pipelines/sundial/data/NC_000962.3.fa.gz --threads=8 --platform=ont --model_path=/home/ubuntu/miniconda3/envs/clair3/bin/models/r941_prom_sup_g5014 --include_all_ctgs --print_ref_calls --gvcf --no_phasing_for_fa --output=clair_out/4
+##reference=/home/ubuntu/pipelines/sundial/data/NC_000962.3.fa.gz
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##FILTER=<ID=LowQual,Description="Low quality variant">
 ##FILTER=<ID=RefCall,Description="Reference call">
diff --git a/tests/nextflow/process_call_all.nf.test b/tests/nextflow/process_call_all.nf.test
index 11cf6e0..3e90db2 100644
--- a/tests/nextflow/process_call_all.nf.test
+++ b/tests/nextflow/process_call_all.nf.test
@@ -10,8 +10,7 @@ nextflow_process {
             }
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
@@ -30,8 +29,7 @@ nextflow_process {
             }
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
@@ -48,8 +46,7 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/not_exist.fastq.gz")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/not_exist.fastq.gz"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
diff --git a/tests/nextflow/process_call_snps.nf.test b/tests/nextflow/process_call_snps.nf.test
index b249a10..9303aa0 100644
--- a/tests/nextflow/process_call_snps.nf.test
+++ b/tests/nextflow/process_call_snps.nf.test
@@ -10,8 +10,7 @@ nextflow_process {
             }
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
@@ -30,8 +29,7 @@ nextflow_process {
             }
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
@@ -48,8 +46,7 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/not_exist.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/not_exist.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
diff --git a/tests/nextflow/process_clair3.nf.test b/tests/nextflow/process_clair3.nf.test
index dd74a8c..374c322 100644
--- a/tests/nextflow/process_clair3.nf.test
+++ b/tests/nextflow/process_clair3.nf.test
@@ -7,9 +7,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
-                input[2] = "$projectDir/data/clair3_models/r1041_e82_400bps_sup_v430.tar.gz"
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/final.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
+                input[1] = "$projectDir/data/clair3_models/r1041_e82_400bps_sup_v430.tar.gz"
                 """
             }
         }
@@ -25,9 +24,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/non_exist.bam")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
-                input[2] = "$projectDir/data/clair3_models/r1041_e82_400bps_sup_v430.tar.gz"
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/non_exist.bam"), file("$projectDir/data/NC_000962.3.fa.gz")]
+                input[1] = "$projectDir/data/clair3_models/r1041_e82_400bps_sup_v430.tar.gz"
                 """
             }
         }
diff --git a/tests/nextflow/process_clair3_consensus.nf.test b/tests/nextflow/process_clair3_consensus.nf.test
index 8b8f0a5..77c2b9d 100644
--- a/tests/nextflow/process_clair3_consensus.nf.test
+++ b/tests/nextflow/process_clair3_consensus.nf.test
@@ -7,9 +7,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/clair3_consensus/bcftools.vcf"), file("$projectDir/test_data/clair3_consensus/clair3.vcf")]
-                input[1] = file("$projectDir/test_data/clair3_consensus/ref.fasta.gz")
-                input[2] = file("$projectDir/test_data/clair3_consensus/consensus_params.yml")
+                input[0] = ['sample', file("$projectDir/test_data/clair3_consensus/bcftools.vcf"), file("$projectDir/test_data/clair3_consensus/clair3.vcf"), file("$projectDir/test_data/clair3_consensus/ref.fasta.gz")]
+                input[1] = file("$projectDir/test_data/clair3_consensus/consensus_params.yml")
                 """
             }
         }
@@ -31,9 +30,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/non_existent.vcf")]
-                input[1] = file("$projectDir/test_data/test_ref.fasta.gz")
-                input[2] = file("$projectDir/test_data/clair3_consensus/consensus_params.yml")
+                input[0] = ['sample', file("$projectDir/test_data/non_existent.vcf"), file("$projectDir/test_data/test_ref.fasta.gz")]
+                input[1] = file("$projectDir/test_data/clair3_consensus/consensus_params.yml")
                 """
             }
         }
diff --git a/tests/nextflow/process_consensus.nf.test b/tests/nextflow/process_consensus.nf.test
index 1a2e965..b2b6e88 100644
--- a/tests/nextflow/process_consensus.nf.test
+++ b/tests/nextflow/process_consensus.nf.test
@@ -7,9 +7,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/single_consensus/consensus_input.vcf")]
-                input[1] = file("$projectDir/test_data/single_consensus/consensus_ref.fasta")
-                input[2] = file("$projectDir/test_data/single_consensus/consensus_params.yml")
+                input[0] = ['sample', file("$projectDir/test_data/single_consensus/consensus_input.vcf"), file("$projectDir/test_data/single_consensus/consensus_ref.fasta")]
+                input[1] = file("$projectDir/test_data/single_consensus/consensus_params.yml")
                 """
             }
         }
@@ -27,9 +26,8 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/single_consensus/non_existent.vcf")]
-                input[1] = file("$projectDir/test_data/single_consensus/consensus_ref.fasta")
-                input[2] = file("$projectDir/test_data/single_consensus/consensus_params.yml")
+                input[0] = ['sample', file("$projectDir/test_data/single_consensus/non_existent.vcf"), file("$projectDir/test_data/single_consensus/non_existent.fasta")]
+                input[1] = file("$projectDir/test_data/single_consensus/consensus_params.yml")
                 """
             }
         }
diff --git a/tests/nextflow/process_minimap2.nf.test b/tests/nextflow/process_minimap2.nf.test
index 3167fb1..cc7492f 100644
--- a/tests/nextflow/process_minimap2.nf.test
+++ b/tests/nextflow/process_minimap2.nf.test
@@ -7,8 +7,7 @@ nextflow_process {
         when {
             process{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/ont_simple.fastq.gz")]
-                input[1] = file("$projectDir/data/h37rv_20231215.fa.gz")
+                input[0] = ['sample', file("$projectDir/test_data/assemblers/ont_simple.fastq.gz"), file("$projectDir/data/NC_000962.3.fa.gz")]
                 """
             }
         }
diff --git a/tests/nextflow/workflow_clair3.nf.test b/tests/nextflow/workflow_clair3.nf.test
index a01f932..289ea34 100644
--- a/tests/nextflow/workflow_clair3.nf.test
+++ b/tests/nextflow/workflow_clair3.nf.test
@@ -7,10 +7,13 @@ nextflow_workflow {
         when {
             workflow{
                 """
-                input[0] = Channel.of(['sample', file("$projectDir/test_data/assemblers/ont_simple.fastq.gz")])
-                input[1] = "$projectDir/data/h37rv_20231215.fa.gz"
-                input[2] = "$projectDir/data/clair3_models"
-                input[3] = "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
+                input[0] = Channel.of(['sample', 
+                                       file("$projectDir/test_data/assemblers/ont_simple.fastq.gz"),                                       
+                                       'Mycobacterium tuberculosis', 
+                                       'NC_000962.3',
+                                       file("$projectDir/data/NC_000962.3.fa.gz")])
+                input[1] = "$projectDir/data/clair3_models"
+                input[2] = "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
                 """
             }
         }
@@ -24,14 +27,17 @@ nextflow_workflow {
         }
     }
 
-    test("Workflow runs falls back to sundial succesfully") {
+    test("Workflow runs falls back to bcftools variant calling succesfully") {
         when {
             workflow{
                 """
-                input[0] = Channel.of(['sample', file("$projectDir/test_data/assemblers/ont_simple.fastq.gz")])
-                input[1] = "$projectDir/data/h37rv_20231215.fa.gz"
-                input[2] = "$projectDir/data/clair3_models"
-                input[3] = "invalid"
+                input[0] = Channel.of(['sample', 
+                                       file("$projectDir/test_data/assemblers/ont_simple.fastq.gz"),                                       
+                                       'Mycobacterium tuberculosis', 
+                                       'NC_000962.3',
+                                       file("$projectDir/data/NC_000962.3.fa.gz")])
+                input[1] = "$projectDir/data/clair3_models"
+                input[2] = "invalid"
                 """
             }
         }
@@ -50,10 +56,13 @@ nextflow_workflow {
         when {
             workflow{
                 """
-                input[0] = ['sample', file("$projectDir/tests/samples/non_existent.fastq.gz")]
-                input[1] = "$projectDir/data/h37rv_20231215.fa.gz"
-                input[2] = "$projectDir/data/clair3_models"
-                input[3] = "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
+                input[0] = Channel.of(['sample', 
+                                       file("$projectDir/tests/samples/non_existent.fastq.gz"),                                       
+                                       'Mycobacterium tuberculosis', 
+                                       'NC_000962.3',
+                                       file("$projectDir/data/NC_000962.3.fa.gz")])
+                input[1] = "$projectDir/data/clair3_models"
+                input[2] = "dna_r10.4.1_e8.2_400bps_sup@v4.3.0"
                 """
             }
         }
diff --git a/tests/nextflow/workflow_rundial_with_bcftools.nf.test b/tests/nextflow/workflow_rundial_with_bcftools.nf.test
index 45075ec..9a60b31 100644
--- a/tests/nextflow/workflow_rundial_with_bcftools.nf.test
+++ b/tests/nextflow/workflow_rundial_with_bcftools.nf.test
@@ -7,8 +7,11 @@ nextflow_workflow {
         when {
             workflow{
                 """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/ont_simple.fastq.gz")]
-                input[1] = "$projectDir/data/h37rv_20231215.fa.gz"
+                input[0] = Channel.of(['sample', 
+                            file("$projectDir/test_data/assemblers/ont_simple.fastq.gz"), 
+                            file("$projectDir/data/NC_000962.3.fa.gz"),
+                            'Mycobacterium tuberculosis', 
+                            'NC_000962.3'])
                 """
             }
         }
@@ -26,9 +29,12 @@ nextflow_workflow {
     test("Workflow should generate error if files do not exist") {
         when {
             workflow{
-                """
-                input[0] = ['sample', file("$projectDir/test_data/assemblers/non_existent.fastq.gz")]
-                input[1] = "$projectDir/data/h37rv_20231215.fa.gz"
+                """                
+                input[0] = Channel.of(['sample', 
+                                       file("$projectDir/test_data/assemblers/non_existent.fastq.gz"), 
+                                       file("$projectDir/data/NC_000962.3.fa.gz"),
+                                       'Mycobacterium tuberculosis', 
+                                       'NC_000962.3'])
                 """
             }
         }