diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml
index 2085c2db293..703b99a0985 100644
--- a/modules/nf-core/gatk4/haplotypecaller/meta.yml
+++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml
@@ -39,7 +39,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - fasta:
       type: file
       description: The reference fasta file
@@ -48,7 +48,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - fai:
       type: file
       description: Index of reference fasta file
@@ -57,7 +57,7 @@ input:
       type: map
       description: |
         Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_reference' ]
   - dict:
       type: file
       description: GATK sequence dictionary
@@ -66,7 +66,7 @@ input:
       type: map
       description: |
         Groovy Map containing dbsnp information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp:
       type: file
       description: VCF file containing known sites (optional)
@@ -74,7 +74,7 @@ input:
       type: map
       description: |
         Groovy Map containing dbsnp information
-        e.g. [ id:'test', single_end:false ]
+        e.g. [ id:'test_dbsnp' ]
   - dbsnp_tbi:
       type: file
       description: VCF index of dbsnp (optional)
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
index 8d6ed4cfaff..4f992d1fec2 100644
--- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test
@@ -36,9 +36,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_bam_input") },
             )
         }
 
@@ -69,9 +69,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_input") },
             )
         }
 
@@ -102,9 +102,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_input_with_sites") },
             )
         }
 
@@ -135,9 +135,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 // { assert snapshot(process.out).match() }, // Unstable hashes
-                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") },
-                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") },
-                { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") },
+                { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") },
+                { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") },
+                { assert snapshot(process.out.versions).match("gatk_hc_versions_cram_dragstr_input_with_sites") },
             )
         }
 
diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
index e5349c2db9a..1717eb3a804 100644
--- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
+++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap
@@ -1,20 +1,130 @@
 {
-    "output/gatk4/versions.yml": {
+    "gatk_hc_vcf_cram_dragstr_input_with_sites": {
         "content": [
-            "versions.yml"
+            "test.vcf.gz"
         ],
-        "timestamp": "2023-11-24T12:59:29.843116"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:55.224088"
     },
-    "output/gatk4/test.vcf.gz.tbi": {
+    "gatk_hc_versions_cram_dragstr_input_with_sites": {
         "content": [
-            "test.vcf.gz.tbi"
+            [
+                "versions.yml:md5,efb80fa7f86bca967db1d03fd09aa7de"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:55.239704"
+    },
+    "gatk_hc_versions_cram_input": {
+        "content": [
+            [
+                "versions.yml:md5,efb80fa7f86bca967db1d03fd09aa7de"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:19.109424"
+    },
+    "gatk_hc_vcf_bam_input": {
+        "content": [
+            "test.vcf.gz"
         ],
-        "timestamp": "2023-11-24T12:59:29.840834"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:49:56.682539"
     },
-    "output/gatk4/test.vcf.gz": {
+    "gatk_hc_vcf_cram_input": {
         "content": [
             "test.vcf.gz"
         ],
-        "timestamp": "2023-11-24T12:59:29.832106"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:19.100309"
+    },
+    "gatk_hc_vcf_cram_input_with_sites": {
+        "content": [
+            "test.vcf.gz"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:36.336371"
+    },
+    "gatk_hc_versions_cram_input_with_sites": {
+        "content": [
+            [
+                "versions.yml:md5,efb80fa7f86bca967db1d03fd09aa7de"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:36.365588"
+    },
+    "gatk_hc_vcf_tbi_bam_input": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:49:56.694329"
+    },
+    "gatk_hc_vcf_tbi_cram_input": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:19.103609"
+    },
+    "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:55.230837"
+    },
+    "gatk_hc_versions_bam_input": {
+        "content": [
+            [
+                "versions.yml:md5,efb80fa7f86bca967db1d03fd09aa7de"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:49:56.696393"
+    },
+    "gatk_hc_vcf_tbi_cram_input_with_sites": {
+        "content": [
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-02-02T10:50:36.35909"
     }
 }
\ No newline at end of file