diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index b3e3813c..cff3dbfb 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -2,15 +2,16 @@ process TIDDIT_SV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
+    conda (params.enable_conda ? "bioconda::tiddit=3.0.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
-        'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
+        'https://depot.galaxyproject.org/singularity/tiddit:3.0.0--py39h59fae87_1' :
+        'quay.io/biocontainers/tiddit:3.0.0--py39h59fae87_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input)
     path  fasta
     path  fai
+    path  bwa_index
 
     output:
     tuple val(meta), path("*.vcf")        , emit: vcf
@@ -26,10 +27,12 @@ process TIDDIT_SV {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--ref $fasta" : ""
     """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
     tiddit \\
         --sv \\
         $args \\
-        --bam $bam \\
+        --bam $input \\
         $reference \\
         -o $prefix
 
diff --git a/tests/modules/tiddit/sv/main.nf b/tests/modules/tiddit/sv/main.nf
index 8dae4950..72113427 100644
--- a/tests/modules/tiddit/sv/main.nf
+++ b/tests/modules/tiddit/sv/main.nf
@@ -2,25 +2,40 @@
 
 nextflow.enable.dsl = 2
 
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
 include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
 
 workflow test_tiddit_sv {
-    input = [ 
+    input = [
         [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
     ]
-    
+
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    TIDDIT_SV ( input, fasta, fai )
+    BWA_INDEX( fasta )
+
+    TIDDIT_SV ( input, fasta, fai , BWA_INDEX.out.index)
 }
 
 workflow test_tiddit_sv_no_ref {
-    input = [ 
+    input = [
         [ id:'test' ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] 
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
     ]
 
     TIDDIT_SV ( input, [], [] )
 }
+
+workflow test_tiddit_sv_cram {
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    TIDDIT_SV ( input, fasta, fai )
+}