diff --git a/modules/nf-core/fastme/tests/main.nf.test.snap b/modules/nf-core/fastme/tests/main.nf.test.snap
index e892b351eae..aa8ffbf7ff7 100644
--- a/modules/nf-core/fastme/tests/main.nf.test.snap
+++ b/modules/nf-core/fastme/tests/main.nf.test.snap
@@ -54,10 +54,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:03:04.842045"
     },
     "versions": {
@@ -66,10 +62,6 @@
                 "versions.yml:md5,0e7f28ae349efffa1ef75c2279e975b6"
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:58.72899"
     },
     "stats_boot": {
@@ -90,10 +82,6 @@
                 ""
             ]
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:09:35.813028"
     },
     "setoxin - phylip - with_tree": {
@@ -151,10 +139,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:51.77025"
     },
     "setoxin - phylip - basic": {
@@ -212,10 +196,6 @@
                 ]
             }
         ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
-        },
         "timestamp": "2024-03-19T10:02:44.598308"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
index a14964c9276..45be6226cb2 100644
--- a/modules/nf-core/tcoffee/align/main.nf
+++ b/modules/nf-core/tcoffee/align/main.nf
@@ -57,6 +57,8 @@ process TCOFFEE_ALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch ${prefix}.aln${compress ? '.gz':''}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test
index 4f136283d08..f0b1752ca8f 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test
@@ -11,7 +11,7 @@ nextflow_process {
     tag "famsa/guidetree"
     tag "untar"
 
-    test("fasta - align_sequence") {
+    test("align_sequence - compressed - seatoxin") {
 
         config "./sequence.config"
 
@@ -19,7 +19,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -31,13 +31,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment")},
-                { assert snapshot(process.out.versions).match("versions_uncomp") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
             )
         }
     }
 
-    test("fasta - align_sequence - uncompressed") {
+    test("align_sequence - uncompressed - seatoxin") {
 
         config "./sequence.config"
 
@@ -45,7 +45,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -57,13 +57,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment - uncompressed")},
-                { assert snapshot(process.out.versions).match("versions_comp") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") },
             )
         }
     }
 
-    test("sarscov2 - fasta - align_with_guide_tree") {
+    test("align_with_guide_tree - uncompressed - seatoxin") {
 
         config "./tree.config"
 
@@ -74,7 +74,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                                ]
 
                     """
@@ -86,7 +86,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]}
                 input[2] = [ [:], [], [] ]
@@ -98,14 +98,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment_guidetree")},
-                { assert snapshot(process.out.versions).match("versions_guidetree") }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
             )
         }
 
     }
 
-    test("fasta - align_with_structure") {
+    test("align_with_structure - uncompressed - seatoxin") {
 
         config "./structure.config"
 
@@ -116,7 +116,7 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                                 file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                                 file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
                                ]
 
                     """
@@ -128,7 +128,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [ [:], [] ]
                 input[2] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], [] ,file(dir).listFiles().collect()]}
@@ -148,7 +148,7 @@ nextflow_process {
 
     }
 
-    test("fasta - align_with_lib") {
+    test("align_with_lib - seatoxin") {
 
         config "./lib.config"
 
@@ -156,7 +156,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
@@ -168,10 +168,40 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment - lib") },
-                { assert path(process.out.lib.get(0).get(1)).getText().contains("1ahl") },
-                { assert snapshot(process.out.versions).match("versions_lib") }
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
+                { assert snapshot(process.out.versions).match()
+                }
             )
         }
     }
+
+    test("align_sequence - uncompressed - seatoxin - stub") {
+        options "-stub"
+        config "./sequence.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = [[:],[],[]]
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.alignment,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
index dfef40a7352..ecf8eadbd13 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
@@ -6,125 +6,77 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
         "timestamp": "2024-02-28T19:00:28.712838"
     },
-    "versions_lib": {
+    "align_sequence - uncompressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T14:04:06.031557"
+        "timestamp": "2024-09-16T10:38:34.006567221"
     },
-    "alignment - uncompressed": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln:md5,bd1db08ad04514cc6d1334598c1a6ef0"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:54.582504"
-    },
-    "versions_comp": {
+    "align_sequence - compressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T18:59:54.593312"
+        "timestamp": "2024-09-16T10:38:18.99603304"
     },
-    "versions_guidetree": {
+    "align_with_guide_tree - uncompressed - seatoxin": {
         "content": [
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T19:00:10.618213"
+        "timestamp": "2024-09-16T10:38:48.044669392"
     },
-    "alignment - lib": {
+    "align_with_lib - seatoxin": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
-                ]
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T13:57:39.653762"
+        "timestamp": "2024-09-16T10:47:34.909457138"
     },
-    "alignment": {
+    "align_sequence - uncompressed - seatoxin - stub": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
+                    "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:35.169119"
-    },
-    "versions_uncomp": {
-        "content": [
+            ],
             [
                 "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
-        },
-        "timestamp": "2024-02-28T18:59:35.2062"
-    },
-    "alignment_guidetree": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.aln.gz:md5,93bc8adfcd88f7913718eacc13da8e4a"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-02-28T19:00:10.611489"
+        "timestamp": "2024-09-16T12:55:10.267649283"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/alncompare/main.nf b/modules/nf-core/tcoffee/alncompare/main.nf
index 043158a75ad..e902120f468 100644
--- a/modules/nf-core/tcoffee/alncompare/main.nf
+++ b/modules/nf-core/tcoffee/alncompare/main.nf
@@ -53,6 +53,8 @@ process TCOFFEE_ALNCOMPARE {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch "${prefix}.scores"
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test
index 225a4f12465..66e5f204cbd 100644
--- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "tcoffee"
-    tag "tcoffee/alncompare" 
+    tag "tcoffee/alncompare"
 
     test("seatoxin") {
 
@@ -15,12 +15,36 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'test' ], // meta map
-                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true),
-                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true),
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
                             ]
                 """
             }
-            
+
+        }
+
+        then {
+        assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+        )
+        }
+
+    }
+    test("seatoxin - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true),
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                """
+            }
+
         }
 
         then {
diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
index d1fd92e4304..20fd7a88877 100644
--- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
@@ -1,4 +1,37 @@
 {
+    "seatoxin - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                ],
+                "scores": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T09:48:00.328461809"
+    },
     "seatoxin": {
         "content": [
             {
@@ -26,6 +59,10 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
         "timestamp": "2024-01-22T17:08:59.494237269"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test b/modules/nf-core/tcoffee/consensus/tests/main.nf.test
index 78aa567bf2d..5f013e3f9e7 100644
--- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test
@@ -8,20 +8,20 @@ nextflow_process {
     tag "modules_nfcore"
     tag "tcoffee"
     tag "tcoffee/consensus"
-    tag "tcoffee/align"
+    tag "magus/align"
     tag "pigz"
-    tag "famsa/guidetree"
+    tag "clustalo/guidetree"
     tag "famsa/align"
 
     config "./sequence.config"
 
     setup {
-        run("FAMSA_GUIDETREE") {
-            script "../../../famsa/guidetree/main.nf"
+        run("CLUSTALO_GUIDETREE") {
+            script "../../../clustalo/guidetree/main.nf"
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)                                 
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                             ]
                 """
             }
@@ -31,7 +31,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)                                 
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                             ]
                 input[1] = [[:],[]]
                 input[2] = false
@@ -39,28 +39,27 @@ nextflow_process {
                 """
             }
         }
-        run("TCOFFEE_ALIGN") {
-            script "../../../tcoffee/align/main.nf"
+        run("MAGUS_ALIGN") {
+            script "../../../magus/align/main.nf"
             process {
                 """
-                input[0] = [ [ id:'test' ],
-                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)                                 
+                input[0] = [ [ id:'test2' ],
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                             ]
                 input[1] = [[:],[]]
-                input[2] = [[:],[],[]]
-                input[3] = false
+                input[2] = false
 
                 """
             }
-        }          
+        }
     }
 
     test("consensus - no tree - uncompressed - seatoxin ") {
-       
+
         when {
             process {
                 """
-                msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple()
+                msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple()
                 input[0] = msas
                 input[1] = [[:],[]]
                 input[2] = false
@@ -71,41 +70,32 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                                    process.out.alignment,
-                                    process.out.versions
-                                 ).match()
-                }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") }
             )
         }
     }
 
-     test("consensus - tree - compressed- seatoxin") {
-
+    test("consensus - tree - compressed- seatoxin") {
         when {
             process {
                 """
-                msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple()
+                msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple()
                 input[0] = msas
-                input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]}
+                input[1] = CLUSTALO_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]}
                 input[2] = true
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                                    process.out.alignment,
-                                    process.out.versions
-                                 ).match()
-                }
+                { assert snapshot(process.out.versions).match()},
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }
             )
         }
     }
 
-
      test("consensus - stub") {
 
         options "-stub"
@@ -113,7 +103,7 @@ nextflow_process {
         when {
             process {
                 """
-                msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple()
+                msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple()
                 input[0] = msas
                 input[1] = [[:],[]]
                 input[2] = false
@@ -128,5 +118,5 @@ nextflow_process {
             )
         }
     }
-  
+
 }
diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
index a0fe4f992ac..ed50562d0e6 100644
--- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
@@ -2,23 +2,26 @@
     "consensus - no tree - uncompressed - seatoxin ": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "consensus.aln:md5,ed7fb1f7b7a9cd66e9b0c9d60d1b0e52"
-                ]
-            ],
-            [
+                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
                 "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
             ]
         ],
-        "timestamp": "2024-09-04T13:17:59.621521"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-18T13:54:43.924522245"
     },
     "consensus - stub": {
         "content": [
             {
                 "0": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "consensus.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
                     [
                         {
                             "id": "test"
@@ -27,9 +30,16 @@
                     ]
                 ],
                 "1": [
+                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
                     "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
                 ],
                 "alignment": [
+                    [
+                        {
+                            "id": "test2"
+                        },
+                        "consensus.aln:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ],
                     [
                         {
                             "id": "test"
@@ -38,26 +48,28 @@
                     ]
                 ],
                 "versions": [
+                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
                     "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
                 ]
             }
         ],
-        "timestamp": "2024-09-04T13:18:15.69498"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-18T13:55:25.155000209"
     },
     "consensus - tree - compressed- seatoxin": {
         "content": [
             [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "consensus.aln.gz:md5,ed7fb1f7b7a9cd66e9b0c9d60d1b0e52"
-                ]
-            ],
-            [
+                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
                 "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
             ]
         ],
-        "timestamp": "2024-09-04T13:18:08.240517"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-18T13:55:03.627733582"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/irmsd/main.nf b/modules/nf-core/tcoffee/irmsd/main.nf
index 95e6b61efb4..be6b6a11bc5 100644
--- a/modules/nf-core/tcoffee/irmsd/main.nf
+++ b/modules/nf-core/tcoffee/irmsd/main.nf
@@ -8,8 +8,8 @@ process TCOFFEE_IRMSD {
         'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
 
     input:
-    tuple  val(meta),  file (msa)
-    tuple  val(meta2), file(template), file(structures)
+    tuple  val(meta),  path (msa)
+    tuple  val(meta2), path(template), path(structures)
 
     output:
     tuple val(meta), path ("${prefix}.irmsd"), emit: irmsd
@@ -44,6 +44,8 @@ process TCOFFEE_IRMSD {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${msa.baseName}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch ${prefix}.irmsd
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml
index f55fca748cf..e13e7ddadf3 100644
--- a/modules/nf-core/tcoffee/irmsd/meta.yml
+++ b/modules/nf-core/tcoffee/irmsd/meta.yml
@@ -27,10 +27,18 @@ input:
       type: file
       description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.
       pattern: "*.{aln,fa,fasta,fas}{.gz,}"
+
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing information about the structures
+        e.g. [ id:'test', ... ]
+
   - template:
       type: file
       description: Template file matching the structures to the sequences in the alignment.
       pattern: "*"
+
   - structures:
       type: directory
       description: Directory containing the structures file matching the sequences in the alignment in PDB format
diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
index 55a574a4616..dfb68629535 100644
--- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
@@ -10,31 +10,43 @@ nextflow_process {
     tag "untar"
     tag "pigz/compress"
 
-    test("seatoxin") {
+    setup {
 
-        setup {
+        run("UNTAR") {
+            script "../../../untar/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                            ]
 
-            run("UNTAR") {
-                script "../../../untar/main.nf"
-                process {
-                    """
-                    input[0] = [ [ id:'test' ],
-                                 file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
-                               ]
+                """
+            }
+        }
 
-                    """
-                }
+        run("PIGZ_COMPRESS") {
+            script "../../../pigz/compress/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+
+                """
             }
         }
+    }
+
+    test("seatoxin") {
 
         when {
             process {
                 """
                 input[0] = [
                                 [ id:'test' ], // meta map
-                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
                             ]
-                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
+                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
                 """
             }
 
@@ -51,38 +63,37 @@ nextflow_process {
 
     test("seatoxin - compressed") {
 
-        setup {
-
-            run("UNTAR") {
-                script "../../../untar/main.nf"
-                process {
-                    """
-                    input[0] = [ [ id:'test' ],
-                                 file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
-                               ]
-
-                    """
-                }
+        when {
+            process {
+                """
+                input[0] = PIGZ_COMPRESS.out.archive
+                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
+                """
             }
 
-            run("PIGZ_COMPRESS") {
-                script "../../../pigz/compress/main.nf"
-                process {
-                    """
-                    input[0] = [ [ id:'test' ],
-                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
-                               ]
+        }
 
-                    """
-                }
-            }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.irmsd.get(0).get(1)).getText().contains("1ahl") }
+            )
         }
 
+    }
+
+    test("seatoxin - uncompressed - stub") {
+
+        options "-stub"
+
         when {
             process {
                 """
-                input[0] = PIGZ_COMPRESS.out.archive
-                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
+                input[0] = [
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
                 """
             }
 
@@ -91,7 +102,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.irmsd.get(0).get(1)).getText().contains("1ahl") }
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
index c036642f18a..909d678c5ca 100644
--- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "seatoxin": {
+    "seatoxin - uncompressed - stub": {
         "content": [
             {
                 "0": [
@@ -7,25 +7,29 @@
                         {
                             "id": "test"
                         },
-                        "setoxin.irmsd:md5,a8f49fb2621cdc9fe39690a813ad0ca5"
+                        "setoxin.irmsd:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,60646e38ef71127e3736a06c91c2983f"
+                    "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
                 ],
                 "irmsd": [
                     [
                         {
                             "id": "test"
                         },
-                        "setoxin.irmsd:md5,a8f49fb2621cdc9fe39690a813ad0ca5"
+                        "setoxin.irmsd:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,60646e38ef71127e3736a06c91c2983f"
+                    "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
                 ]
             }
         ],
-        "timestamp": "2023-12-13T12:26:46.827121"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T10:15:36.874290895"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf b/modules/nf-core/tcoffee/seqreformat/main.nf
index c4c31f835f8..04617b01ffd 100644
--- a/modules/nf-core/tcoffee/seqreformat/main.nf
+++ b/modules/nf-core/tcoffee/seqreformat/main.nf
@@ -38,6 +38,8 @@ process TCOFFEE_SEQREFORMAT {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch "${prefix}.txt"
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml
index 9c7d9ce9916..0571c7d875d 100644
--- a/modules/nf-core/tcoffee/seqreformat/meta.yml
+++ b/modules/nf-core/tcoffee/seqreformat/meta.yml
@@ -19,7 +19,7 @@ input:
         Groovy Map containing sample information
         e.g. `[ id:'test' ]`
 
-  - fasta:
+  - infile:
       type: file
       description: Input file to be reformatted
       pattern: "*"
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test
index 7a5492c51ab..1510e92075b 100644
--- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test
@@ -9,13 +9,13 @@ nextflow_process {
     tag "tcoffee"
     tag "tcoffee/seqreformat"
 
-    test("sarscov2 - bam") {
+    test("seatoxin") {
 
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                 """
             }
@@ -25,8 +25,36 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.formatted_file).match("formatted_file")},
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+                    process.out.formatted_file,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("seatoxin - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                """
+            }
+        }
+
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.formatted_file,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
index 150102ee3a8..185f24d8f55 100644
--- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
@@ -1,23 +1,42 @@
 {
-    "formatted_file": {
+    "seatoxin - stub": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562"
+                    "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
+            ],
+            [
+                "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
             ]
         ],
-        "timestamp": "2023-11-28T11:56:22.705185493"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T09:53:55.165479364"
     },
-    "versions": {
+    "seatoxin": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562"
+                ]
+            ],
             [
                 "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
             ]
         ],
-        "timestamp": "2023-11-28T11:56:22.717235196"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T09:53:33.814075197"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml
index 615d140e6bb..26a17e70983 100644
--- a/modules/nf-core/tcoffee/tcs/environment.yml
+++ b/modules/nf-core/tcoffee/tcs/environment.yml
@@ -1,8 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::t-coffee=13.46.0.919e8c6b"
+  - bioconda::t-coffee=13.46.0.919e8c6b
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/tcs/main.nf b/modules/nf-core/tcoffee/tcs/main.nf
index 0c50f52a233..9080a317479 100644
--- a/modules/nf-core/tcoffee/tcs/main.nf
+++ b/modules/nf-core/tcoffee/tcs/main.nf
@@ -8,7 +8,7 @@ process TCOFFEE_TCS {
         'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
 
     input:
-    tuple val(meta), path(msa)
+    tuple val(meta) , path(msa)
     tuple val(meta2), path(lib)
 
     output:
@@ -63,6 +63,8 @@ process TCOFFEE_TCS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Otherwise, tcoffee will crash when calling its version
+    export TEMP='./'
     touch ${prefix}.tcs
     touch ${prefix}.scores
 
diff --git a/modules/nf-core/tcoffee/tcs/meta.yml b/modules/nf-core/tcoffee/tcs/meta.yml
index a28efad0ab8..7a13e79a8b6 100644
--- a/modules/nf-core/tcoffee/tcs/meta.yml
+++ b/modules/nf-core/tcoffee/tcs/meta.yml
@@ -29,6 +29,11 @@ input:
       type: file
       description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.
       pattern: "*.{aln,fa,fasta,fas}{.gz,}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing library information
+        e.g. [ id:'test', ... ]
   - lib:
       type: file
       description: lib file containing the alignment library of the given msa.
diff --git a/modules/nf-core/tcoffee/tcs/tests/lib.config b/modules/nf-core/tcoffee/tcs/tests/lib.config
index 56712f63798..610250ce235 100644
--- a/modules/nf-core/tcoffee/tcs/tests/lib.config
+++ b/modules/nf-core/tcoffee/tcs/tests/lib.config
@@ -1,5 +1,7 @@
 process {
+
     withName: "TCOFFEE_ALIGN"{
         ext.args = { "-output fasta_aln -out_lib sample_lib1.tc_lib" }
     }
+
 }
diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test b/modules/nf-core/tcoffee/tcs/tests/main.nf.test
index 35636fff075..d66a2cdaa31 100644
--- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test
@@ -10,14 +10,14 @@ nextflow_process {
     tag "pigz/compress"
     tag "tcoffee/align"
 
-    test("tcs - msa") {
+    test("tcs - seatoxin") {
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test'], 
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                    [ id:'test'],
+                      file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
                     ]
                 input[1] = [
                     [ id:'test'],
@@ -30,13 +30,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") },
+                { assert snapshot(process.out.versions).match()
+                }
             )
         }
 
     }
 
-    test("tcs - msa - compressed") {
+    test("tcs - seatoxin - compressed") {
 
         setup {
             run("PIGZ_COMPRESS") {
@@ -44,12 +46,12 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                                 file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
                                ]
 
                     """
                 }
-            }        
+            }
         }
 
         when {
@@ -67,12 +69,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") },
+                { assert snapshot(process.out.versions).match()
+                }
             )
         }
     }
 
-    test("tcs - msa - lib") {
+    test("tcs - seatoxin - lib") {
 
         config "./lib.config"
 
@@ -82,33 +86,63 @@ nextflow_process {
                 process {
                     """
                     input[0] = [ [ id:'test' ],
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                               file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
                            ]
                     input[1] = [[:],[]]
                     input[2] = [[:],[],[]]
                     input[3] = true
                     """
                 }
-            }        
+            }
         }
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test'], 
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                    [ id:'test'],
+                      file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
                     ]
                 input[1] = TCOFFEE_ALIGN.out.lib.map { it -> [[  id:'test' ], it[1]] }
                 """
             }
         }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") },
+                { assert snapshot(process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("tcs - seatoxin - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                      file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                    ]
+                input[1] = [
+                    [ id:'test'],
+                    []
+                    ]
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
+
     }
 }
diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
index 8f6fca132c4..80da751875b 100644
--- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
@@ -1,54 +1,17 @@
 {
-    "tcs - msa - lib": {
+    "tcs - seatoxin - compressed": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
-                ],
-                "scores": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
-                    ]
-                ],
-                "tcs": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
-                ]
-            }
+            [
+                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T17:52:51.096817"
+        "timestamp": "2024-09-16T13:13:16.017532678"
     },
-    "tcs - msa": {
+    "tcs - seatoxin - stub": {
         "content": [
             {
                 "0": [
@@ -56,7 +19,7 @@
                         {
                             "id": "test"
                         },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
+                        "test.tcs:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -64,7 +27,7 @@
                         {
                             "id": "test"
                         },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
+                        "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -75,7 +38,7 @@
                         {
                             "id": "test"
                         },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
+                        "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "tcs": [
@@ -83,7 +46,7 @@
                         {
                             "id": "test"
                         },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
+                        "test.tcs:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -92,58 +55,33 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T12:47:34.828638"
+        "timestamp": "2024-09-16T09:59:35.62776554"
     },
-    "tcs - msa - compressed": {
+    "tcs - seatoxin - lib": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
-                ],
-                "scores": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.scores:md5,25576b8e2fef74953d28f4e3df689d93"
-                    ]
-                ],
-                "tcs": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
-                ]
-            }
+            [
+                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-16T13:13:32.306127259"
+    },
+    "tcs - seatoxin": {
+        "content": [
+            [
+                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-19T17:37:52.408687"
+        "timestamp": "2024-09-16T13:13:00.253922777"
     }
 }
\ No newline at end of file