diff --git a/tests/modules/mapping/gem/main.index.nf.test b/tests/modules/mapping/gem/main.index.nf.test
new file mode 100644
index 0000000..9841afc
--- /dev/null
+++ b/tests/modules/mapping/gem/main.index.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process index"
+    script "modules/mapping/gem/main.nf"
+    process "index"
+
+    tag "module"
+
+    test("Should create index using GEM (compressed references)") {
+
+        when {
+            process {
+                """
+                input[0] = file("${baseDir}/data/genome.fa.gz")
+                input[1] = file("${baseDir}/data/annotation.gtf.gz")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            with(process.out) {
+                def genomeDir = get(0)[0]
+                assert path(genomeDir).list().size() == 7
+                assert snapshot(
+                    path("${genomeDir}/genome_index.gem"),
+                    path("${genomeDir}/transcript_index.junctions"),
+                    path("${genomeDir}/transcript_index.junctions.fa"),
+                    path("${genomeDir}/transcript_index.junctions.gem"),
+                    path("${genomeDir}/transcript_index.junctions.keys"),
+                ).match()
+            }
+        }
+
+    }
+
+    test("Should create index using GEM (uncompressed references)") {
+
+        when {
+            process {
+                """
+                input[0] = file("${baseDir}/data/genome.fa")
+                input[1] = file("${baseDir}/data/annotation.gtf")
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            with(process.out) {
+                def genomeDir = get(0)[0]
+                assert path(genomeDir).list().size() == 7
+                assert snapshot(
+                    path("${genomeDir}/genome_index.gem"),
+                    path("${genomeDir}/transcript_index.junctions"),
+                    path("${genomeDir}/transcript_index.junctions.fa"),
+                    path("${genomeDir}/transcript_index.junctions.gem"),
+                    path("${genomeDir}/transcript_index.junctions.keys"),
+                ).match()
+            }
+        }
+
+    }
+
+}
diff --git a/tests/modules/mapping/gem/main.index.nf.test.snap b/tests/modules/mapping/gem/main.index.nf.test.snap
new file mode 100644
index 0000000..47c564f
--- /dev/null
+++ b/tests/modules/mapping/gem/main.index.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "Should create index using GEM (compressed references)": {
+        "content": [
+            "genome_index.gem:md5,ebd155f05251ace3a35ce3edd8816211",
+            "transcript_index.junctions:md5,a0433e39f0c35e798609ff15332e12d4",
+            "transcript_index.junctions.fa:md5,be0a28c75266e6969c11e308341810ae",
+            "transcript_index.junctions.gem:md5,b53971e7b5358fd8cae8bb7f2a4a729d",
+            "transcript_index.junctions.keys:md5,34985e55c280acd027d2dd32906ad59c"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-02T09:01:47.328374722"
+    },
+    "Should create index using GEM (uncompressed references)": {
+        "content": [
+            "genome_index.gem:md5,ebd155f05251ace3a35ce3edd8816211",
+            "transcript_index.junctions:md5,a0433e39f0c35e798609ff15332e12d4",
+            "transcript_index.junctions.fa:md5,be0a28c75266e6969c11e308341810ae",
+            "transcript_index.junctions.gem:md5,b53971e7b5358fd8cae8bb7f2a4a729d",
+            "transcript_index.junctions.keys:md5,34985e55c280acd027d2dd32906ad59c"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-02T09:02:27.226869622"
+    }
+}
\ No newline at end of file
diff --git a/tests/modules/mapping/gem/main.map.nf.test b/tests/modules/mapping/gem/main.map.nf.test
new file mode 100644
index 0000000..09aacad
--- /dev/null
+++ b/tests/modules/mapping/gem/main.map.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process map"
+    script "modules/mapping/gem/main.nf"
+    process "map"
+
+    tag "module"
+
+    setup {
+        run("index") {
+            script "modules/mapping/gem/main.nf"
+            process {
+                """
+                input[0] = file("${baseDir}/data/genome.fa")
+                input[1] = file("${baseDir}/data/annotation.gtf")
+                """
+            }
+        }
+    }
+
+    test("Should align reads to the reference using GEM (compressed annotation)") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+            }
+            process {
+                """
+                def fastqs = file("${baseDir}/data/test1_*.fastq.gz")
+                def qScore = fastq(fastqs[0]).qualityScore()
+                input[0] = file("${baseDir}/data/annotation.gtf.gz")
+                input[1] = index.out
+                input[2] = Channel.from(
+                    [
+                        [ "sample1", "test1", fastqs, "fastq", ["fqRd1", "fqRd2"], qScore]
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+    test("Should align reads to the reference using GEM (uncompressed annotation)") {
+
+        when {
+            params {
+                maxMismatches = 4
+                maxMultimaps = 10
+            }
+            process {
+                """
+                def fastqs = file("${baseDir}/data/test1_*.fastq.gz")
+                def qScore = fastq(fastqs[0]).qualityScore()
+                input[0] = file("${baseDir}/data/annotation.gtf")
+                input[1] = index.out
+                input[2] = Channel.from(
+                    [
+                        [ "sample1", "test1", fastqs, "fastq", ["fqRd1", "fqRd2"], qScore]
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
diff --git a/tests/modules/mapping/gem/main.map.nf.test.snap b/tests/modules/mapping/gem/main.map.nf.test.snap
new file mode 100644
index 0000000..4e82cd3
--- /dev/null
+++ b/tests/modules/mapping/gem/main.map.nf.test.snap
@@ -0,0 +1,140 @@
+{
+    "Should align reads to the reference using GEM (compressed annotation)": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam:md5,48faeddd5179ce7b5d629ad937851b45",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam.bai:md5,f0b712d99d68ae3132bdb287ed5a5e5d",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "genomeAlignments": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam:md5,48faeddd5179ce7b5d629ad937851b45",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "genomeAlignmentsIndices": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam.bai:md5,f0b712d99d68ae3132bdb287ed5a5e5d",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ],
+                "junctions": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "transcriptomeAlignments": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-02T08:54:34.740923082"
+    },
+    "Should align reads to the reference using GEM (uncompressed annotation)": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam:md5,48faeddd5179ce7b5d629ad937851b45",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam.bai:md5,f0b712d99d68ae3132bdb287ed5a5e5d",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "genomeAlignments": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam:md5,48faeddd5179ce7b5d629ad937851b45",
+                        "bam",
+                        "GenomeAlignments",
+                        true
+                    ]
+                ],
+                "genomeAlignmentsIndices": [
+                    [
+                        "sample1",
+                        "test1",
+                        "sample1_m4_n10_toGenome.bam.bai:md5,f0b712d99d68ae3132bdb287ed5a5e5d",
+                        "bai",
+                        "GenomeAlignmentsIndex",
+                        true
+                    ]
+                ],
+                "junctions": [
+                    
+                ],
+                "stats": [
+                    
+                ],
+                "transcriptomeAlignments": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-02T08:55:30.059497532"
+    }
+}
\ No newline at end of file
diff --git a/tests/modules/mapping/star/main.index.nf.test b/tests/modules/mapping/star/main.index.nf.test
index 466c4f8..029b2f8 100644
--- a/tests/modules/mapping/star/main.index.nf.test
+++ b/tests/modules/mapping/star/main.index.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
 
     tag "module"
 
-    test("Should index compressed references") {
+    test("Should create index using STAR (compressed references)") {
 
         when {
             params {
@@ -47,7 +47,7 @@ nextflow_process {
 
     }
 
-    test("Should index uncompressed references") {
+    test("Should create index using STAR (uncompressed references)") {
 
         when {
             params {
diff --git a/tests/modules/mapping/star/main.index.nf.test.snap b/tests/modules/mapping/star/main.index.nf.test.snap
index 1ac2c66..dba0439 100644
--- a/tests/modules/mapping/star/main.index.nf.test.snap
+++ b/tests/modules/mapping/star/main.index.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should index compressed references": {
+    "Should create index using STAR (compressed references)": {
         "content": [
             "Genome:md5,7ede3c93094305c2b5c18e2f52110194",
             "SA:md5,66c24435d4e28eeddb6a5014ac90c4ef",
@@ -23,7 +23,7 @@
         },
         "timestamp": "2024-04-17T17:20:31.357378"
     },
-    "Should index uncompressed references": {
+    "Should create index using STAR (uncompressed references)": {
         "content": [
             "Genome:md5,7ede3c93094305c2b5c18e2f52110194",
             "SA:md5,66c24435d4e28eeddb6a5014ac90c4ef",
@@ -47,4 +47,4 @@
         },
         "timestamp": "2024-04-17T17:20:43.134729"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/modules/mapping/star/main.map.nf.test b/tests/modules/mapping/star/main.map.nf.test
index d5955f1..a12090b 100644
--- a/tests/modules/mapping/star/main.map.nf.test
+++ b/tests/modules/mapping/star/main.map.nf.test
@@ -18,11 +18,10 @@ nextflow_process {
         }
     }
 
-    test("Should align reads to the reference with compressed annotation") {
+    test("Should align reads to the reference using STAR (compressed annotation)") {
 
         when {
             params {
-                mappingTool  = "STAR"
                 sjOverHang = 100
                 quantificationTool = "RSEM"
                 maxMismatches = 4
@@ -53,11 +52,10 @@ nextflow_process {
 
     }
 
-    test("Should align reads to the reference with uncompressed annotation") {
+    test("Should align reads to the reference using STAR (uncompressed annotation)") {
 
         when {
             params {
-                mappingTool  = "STAR"
                 sjOverHang = 100
                 quantificationTool = "RSEM"
                 maxMismatches = 4
diff --git a/tests/modules/mapping/star/main.map.nf.test.snap b/tests/modules/mapping/star/main.map.nf.test.snap
index 87be468..cc27f6e 100644
--- a/tests/modules/mapping/star/main.map.nf.test.snap
+++ b/tests/modules/mapping/star/main.map.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should align reads to the reference with uncompressed annotation": {
+    "Should align reads to the reference using STAR (uncompressed annotation)": {
         "content": [
             [
                 [
@@ -12,7 +12,7 @@
                 ]
             ],
             [
-                
+
             ],
             [
                 [
@@ -41,7 +41,7 @@
         },
         "timestamp": "2024-04-23T23:19:28.403716"
     },
-    "Should align reads to the reference with compressed annotation": {
+    "Should align reads to the reference using STAR (compressed annotation)": {
         "content": [
             [
                 [
@@ -54,7 +54,7 @@
                 ]
             ],
             [
-                
+
             ],
             [
                 [
@@ -83,4 +83,4 @@
         },
         "timestamp": "2024-04-23T23:11:13.889531"
     }
-}
\ No newline at end of file
+}