diff --git a/modules/nf-core/goleft/indexcov/environment.yml b/modules/nf-core/goleft/indexcov/environment.yml
index b5799272031..691377901c8 100644
--- a/modules/nf-core/goleft/indexcov/environment.yml
+++ b/modules/nf-core/goleft/indexcov/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::goleft=0.2.4
+  - bioconda::htslib=1.12
diff --git a/modules/nf-core/goleft/indexcov/main.nf b/modules/nf-core/goleft/indexcov/main.nf
index c01ec657122..5d0ed5dfb01 100644
--- a/modules/nf-core/goleft/indexcov/main.nf
+++ b/modules/nf-core/goleft/indexcov/main.nf
@@ -12,13 +12,14 @@ process GOLEFT_INDEXCOV {
     tuple val(meta2), path(fai)
 
     output:
-    tuple val(meta), path("${prefix}/*")      , emit: output
-    tuple val(meta), path("${prefix}/*ped")   , emit: ped , optional: true
-    tuple val(meta), path("${prefix}/*bed.gz"), emit: bed , optional: true
-    tuple val(meta), path("${prefix}/*roc")   , emit: roc , optional: true
-    tuple val(meta), path("${prefix}/*html")  , emit: html, optional: true
-    tuple val(meta), path("${prefix}/*png")   , emit: png , optional: true
-    path "versions.yml"                      , emit: versions
+    tuple val(meta), path("${prefix}/*")          , emit: output
+    tuple val(meta), path("${prefix}/*ped")       , emit: ped , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz")    , emit: bed , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz.tbi"), emit: bed_index , optional: true
+    tuple val(meta), path("${prefix}/*roc")       , emit: roc , optional: true
+    tuple val(meta), path("${prefix}/*html")      , emit: html, optional: true
+    tuple val(meta), path("${prefix}/*png")       , emit: png , optional: true
+    path "versions.yml"                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,9 +38,14 @@ process GOLEFT_INDEXCOV {
         $args \\
         ${input_files.join(" ")}
 
+    if [ -f "${prefix}/${prefix}-indexcov.bed.gz" ] ; then
+        tabix -p bed "${prefix}/${prefix}-indexcov.bed.gz"
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
     stub:
@@ -47,11 +53,13 @@ process GOLEFT_INDEXCOV {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir "${prefix}"
-    touch "${prefix}/${prefix}-indexcov.bed.gz"
+    echo "" | gzip > "${prefix}/${prefix}-indexcov.bed.gz"
+    touch "${prefix}/${prefix}-indexcov.bed.gz.tbi"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test b/modules/nf-core/goleft/indexcov/tests/main.nf.test
index eb458a52b7d..1296c644cd2 100644
--- a/modules/nf-core/goleft/indexcov/tests/main.nf.test
+++ b/modules/nf-core/goleft/indexcov/tests/main.nf.test
@@ -18,11 +18,11 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     [
                         file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true),
-                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)                                                                                       
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
                     ],
                     [
                         file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true),
-                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)                                                                                       
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
                     ],
                 ])
 
@@ -39,7 +39,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -76,7 +84,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
             )
         }
 
@@ -105,7 +121,8 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap b/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap
index 2ef54ab6b15..1c79232db0d 100644
--- a/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap
+++ b/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap
@@ -1,223 +1,65 @@
 {
     "sarscov2 - crai": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "index.html:md5,41840ede180b20cdf6074c431269929e",
-                            "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
-                            "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
-                            "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450",
-                            "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698",
-                            "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589",
-                            "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791",
-                            "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
-                    ]
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "index.html:md5,41840ede180b20cdf6074c431269929e",
-                            "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
-                            "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450"
-                        ]
-                    ]
-                ],
-                "5": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
-                            "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698"
-                        ]
-                    ]
-                ],
-                "6": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589"
-                    ]
-                ],
-                "html": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "index.html:md5,41840ede180b20cdf6074c431269929e",
-                            "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
-                            "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450"
-                        ]
-                    ]
-                ],
-                "output": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "index.html:md5,41840ede180b20cdf6074c431269929e",
-                            "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
-                            "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
-                            "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450",
-                            "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698",
-                            "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589",
-                            "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791",
-                            "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
-                        ]
-                    ]
-                ],
-                "ped": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791"
-                    ]
-                ],
-                "png": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
-                            "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698"
-                        ]
-                    ]
-                ],
-                "roc": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791"
                 ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-08-02T17:12:40.654571"
-    },
-    "sarscov2 - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/adam.talbot/modules/.nf-test/tests/b176772886dc6c01086acecdcebb9167/work/bf/334844199c0739497d80a21d7e4743/test/test-indexcov.bed.gz"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/adam.talbot/modules/.nf-test/tests/b176772886dc6c01086acecdcebb9167/work/bf/334844199c0739497d80a21d7e4743/test/test-indexcov.bed.gz"
-                    ]
-                ],
-                "3": [
-                    
-                ],
-                "4": [
-                    
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
-                ],
-                "bed": [
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589"
+                ]
+            ],
+            "test-indexcov.bed.gz.tbi",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
                     [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/adam.talbot/modules/.nf-test/tests/b176772886dc6c01086acecdcebb9167/work/bf/334844199c0739497d80a21d7e4743/test/test-indexcov.bed.gz"
+                        "index.html:md5,41840ede180b20cdf6074c431269929e",
+                        "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
+                        "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450"
                     ]
-                ],
-                "html": [
-                    
-                ],
-                "output": [
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
                     [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/adam.talbot/modules/.nf-test/tests/b176772886dc6c01086acecdcebb9167/work/bf/334844199c0739497d80a21d7e4743/test/test-indexcov.bed.gz"
+                        "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
+                        "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698"
                     ]
-                ],
-                "ped": [
-                    
-                ],
-                "png": [
-                    
-                ],
-                "roc": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
                 ]
-            }
+            ],
+            [
+                "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+            ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T17:16:50.485859"
+        "timestamp": "2024-08-22T06:40:17.142801459"
     },
-    "sarscov2 - bam": {
+    "sarscov2 - stub": {
         "content": [
             {
                 "0": [
@@ -226,27 +68,20 @@
                             "id": "test"
                         },
                         [
-                            "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e",
-                            "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029",
-                            "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9",
-                            "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
+                            "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9"
-                    ]
+                    
                 ],
                 "2": [
                     [
                         {
                             "id": "test"
                         },
-                        "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029"
+                        "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "3": [
@@ -254,38 +89,39 @@
                         {
                             "id": "test"
                         },
-                        "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
+                        "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "4": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e"
-                    ]
+                    
                 ],
                 "5": [
                     
                 ],
                 "6": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
+                    
+                ],
+                "7": [
+                    "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
                 ],
                 "bed": [
                     [
                         {
                             "id": "test"
                         },
-                        "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029"
+                        "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "html": [
+                "bed_index": [
                     [
                         {
                             "id": "test"
                         },
-                        "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e"
+                        "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
+                ],
+                "html": [
+                    
                 ],
                 "output": [
                     [
@@ -293,41 +129,77 @@
                             "id": "test"
                         },
                         [
-                            "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e",
-                            "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029",
-                            "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9",
-                            "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
+                            "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                         ]
                     ]
                 ],
                 "ped": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9"
-                    ]
+                    
                 ],
                 "png": [
                     
                 ],
                 "roc": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,97bf6a6d60aca3de3773d8a0fbf053a1"
+                    "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.2"
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T06:44:59.203730744"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029"
+                ]
+            ],
+            "test-indexcov.bed.gz.tbi",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T16:52:31.400233"
+        "timestamp": "2024-08-22T06:39:48.470187823"
     }
 }
\ No newline at end of file