diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf
index 7919678c..f08d4d91 100644
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/gatk4/getpileupsummaries/main.nf
@@ -21,7 +21,7 @@ process GATK4_GETPILEUPSUMMARIES {
     input:
     tuple val(meta), path(bam), path(bai)
     path variants
-    path variants_idx
+    path variants_tbi
     path sites
 
     output:
diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml
index 70158a8d..0add299b 100644
--- a/modules/gatk4/getpileupsummaries/meta.yml
+++ b/modules/gatk4/getpileupsummaries/meta.yml
@@ -35,7 +35,7 @@ input:
       type: file
       description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
       pattern: "*.vcf.gz"
-  - variants_idx:
+  - variants_tbi:
       type: file
       description: Index file for the germline resource.
       pattern: "*.vcf.gz.tbi"
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index 748b1673..dd8da406 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -28,9 +28,9 @@ process GATK4_MUTECT2 {
     path fastaidx
     path dict
     path germline_resource
-    path germline_resource_idx
+    path germline_resource_tbi
     path panel_of_normals
-    path panel_of_normals_idx
+    path panel_of_normals_tbi
 
     output:
     tuple val(meta), path("*.vcf.gz")     , emit: vcf
diff --git a/modules/gatk4/mutect2/meta.yml b/modules/gatk4/mutect2/meta.yml
index 44601e41..4a49b07a 100644
--- a/modules/gatk4/mutect2/meta.yml
+++ b/modules/gatk4/mutect2/meta.yml
@@ -66,18 +66,18 @@ input:
       type: file
       description: Population vcf of germline sequencing, containing allele fractions.
       pattern: "*.vcf.gz"
-  - germline_resource_idx:
+  - germline_resource_tbi:
       type: file
       description: Index file for the germline resource.
-      pattern: "*.vcf.gz_tbi"
+      pattern: "*.vcf.gz.tbi"
   - panel_of_normals:
       type: file
       description: vcf file to be used as a panel of normals.
       pattern: "*.vcf.gz"
-  - panel_of_normals_idx:
+  - panel_of_normals_tbi:
       type: file
       description: Index for the panel of normals.
-      pattern: "*.vcf.gz_tbi"
+      pattern: "*.vcf.gz.tbi"
 
 output:
   - vcf:
diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf
index 0c7d3fb6..66ee4990 100644
--- a/tests/modules/gatk4/getpileupsummaries/main.nf
+++ b/tests/modules/gatk4/getpileupsummaries/main.nf
@@ -11,10 +11,10 @@ workflow test_gatk4_getpileupsummaries_just_variants {
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
 
     variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
-    variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
+    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     sites = []
 
-    GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
+    GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
 }
 
 workflow test_gatk4_getpileupsummaries_separate_sites {
@@ -24,8 +24,8 @@ workflow test_gatk4_getpileupsummaries_separate_sites {
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
 
     variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
-    variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
+    variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     sites = file( "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" , checkIfExists: true)
 
-    GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
+    GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites )
 }
diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 293739e4..a3821b64 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -20,11 +20,11 @@ workflow test_gatk4_mutect2_tumor_normal_pair {
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
-    germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
-    panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_TEMPFIX_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
+    GATK4_TEMPFIX_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_tumor_single {
@@ -41,11 +41,11 @@ workflow test_gatk4_mutect2_tumor_single {
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
-    germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
-    panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
+    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_cram_input {
@@ -62,11 +62,11 @@ workflow test_gatk4_mutect2_cram_input {
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
-    germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
     panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
-    panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
 
-    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
+    GATK4_MUTECT2 ( input , run_single , run_pon , run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
 }
 
 workflow test_gatk4_mutect2_generate_pon {
@@ -83,11 +83,11 @@ workflow test_gatk4_mutect2_generate_pon {
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = []
-    germline_resource_idx = []
+    germline_resource_tbi = []
     panel_of_normals = []
-    panel_of_normals_idx = []
+    panel_of_normals_tbi = []
 
-    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
+    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
 }
 
 // mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working.
@@ -105,9 +105,9 @@ workflow test_gatk4_mutect2_mitochondria {
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     germline_resource = []
-    germline_resource_idx = []
+    germline_resource_tbi = []
     panel_of_normals = []
-    panel_of_normals_idx = []
+    panel_of_normals_tbi = []
 
-    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
+    GATK4_MUTECT2 ( input , run_single , run_pon, run_mito , interval_label , fasta , fastaidx , dict , germline_resource, germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
 }