diff --git a/modules/nf-core/genomad/download/environment.yml b/modules/nf-core/genomad/download/environment.yml
index eacd45d0f81..5c9b27a8405 100644
--- a/modules/nf-core/genomad/download/environment.yml
+++ b/modules/nf-core/genomad/download/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::genomad=1.5.2
+  - bioconda::genomad=1.7.4
diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf
index 7e7b12ed437..d5717e390ad 100644
--- a/modules/nf-core/genomad/download/main.nf
+++ b/modules/nf-core/genomad/download/main.nf
@@ -3,8 +3,8 @@ process GENOMAD_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genomad:1.7.4--pyhdfd78af_0':
+        'biocontainers/genomad:1.7.4--pyhdfd78af_0' }"
 
     output:
     path "genomad_db/"  , emit: genomad_db
diff --git a/modules/nf-core/genomad/download/meta.yml b/modules/nf-core/genomad/download/meta.yml
index 6a527eb55de..5df21ee6a80 100644
--- a/modules/nf-core/genomad/download/meta.yml
+++ b/modules/nf-core/genomad/download/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://portal.nersc.gov/genomad/
       tool_dev_url: https://github.com/apcamargo/genomad/
       doi: 10.1101/2023.03.05.531206
-      licence: "['Lawrence Berkeley National Labs BSD variant license']"
+      licence: ["Lawrence Berkeley National Labs BSD variant license"]
 output:
   - versions:
       type: file
diff --git a/modules/nf-core/genomad/download/tests/main.nf.test b/modules/nf-core/genomad/download/tests/main.nf.test
new file mode 100644
index 00000000000..18456f6119b
--- /dev/null
+++ b/modules/nf-core/genomad/download/tests/main.nf.test
@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test Process GENOMAD_DOWNLOAD"
+    script "../main.nf"
+    process "GENOMAD_DOWNLOAD"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genomad"
+    tag "genomad/download"
+
+    test("No input") {
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("No input - stub") {
+
+        options "-stub"
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/genomad/download/tests/main.nf.test.snap b/modules/nf-core/genomad/download/tests/main.nf.test.snap
new file mode 100644
index 00000000000..320bef8832b
--- /dev/null
+++ b/modules/nf-core/genomad/download/tests/main.nf.test.snap
@@ -0,0 +1,190 @@
+{
+    "No input - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "genomad_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_marker_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "mini_set_ids:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "plasmid_hallmark_annotation.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "version.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "virus_hallmark_annotation.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e98d6885d0b88a7a71f288fcff0b7b14"
+                ],
+                "genomad_db": [
+                    [
+                        "genomad_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_db_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_integrase_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_marker_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.lookup:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db.source:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_h.index:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_mapping:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "genomad_mini_db_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "mini_set_ids:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "plasmid_hallmark_annotation.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "version.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "virus_hallmark_annotation.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e98d6885d0b88a7a71f288fcff0b7b14"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-03T17:41:56.803756044"
+    },
+    "No input": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            "version-checkpoint.txt:md5,6527da533ace4cb4473cc907f265f170"
+                        ],
+                        "genomad_db:md5,b9ce17f8b01203c37a9147b5294dace6",
+                        "genomad_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_db.index:md5,5693ab7d5fe2c7947a9a43a9b5705f55",
+                        "genomad_db.lookup:md5,973c8434e0cf70593af1f888c4424876",
+                        "genomad_db.source:md5,6805958c7c99a8e8ab38095a40dc0081",
+                        "genomad_db_h:md5,1325d5db1da081c479a455a3e7440ae4",
+                        "genomad_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_db_h.index:md5,8c14ed8d3b520be4cd22340a250d26bf",
+                        "genomad_db_mapping:md5,2e10dbb66f99183ff42092777a8089ca",
+                        "genomad_db_taxonomy:md5,5abcff23ab2efa5f5dcfc37cc55ccbbc",
+                        "genomad_integrase_db:md5,23e19f271d2d65261588821a1e7d2b30",
+                        "genomad_integrase_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_integrase_db.index:md5,7bae797a783d3f12c75845130ccb9b8a",
+                        "genomad_integrase_db.lookup:md5,cc0702fcafb9a0b27992fd54fc699d25",
+                        "genomad_integrase_db.source:md5,b6ff391f60a2d9d615c7eb41fbf01c19",
+                        "genomad_integrase_db_h:md5,118e59c1b7bbbdfa6776c17da3db430b",
+                        "genomad_integrase_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_integrase_db_h.index:md5,2e8987568dae1a3f4c0207657fd84205",
+                        "genomad_marker_metadata.tsv:md5,fcf64cdbfcd0e099b44143ff99133fed",
+                        "genomad_mini_db:md5,b9ce17f8b01203c37a9147b5294dace6",
+                        "genomad_mini_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_mini_db.index:md5,e62e3de510ea7f5e73038f51ab02330f",
+                        "genomad_mini_db.lookup:md5,973c8434e0cf70593af1f888c4424876",
+                        "genomad_mini_db.source:md5,6805958c7c99a8e8ab38095a40dc0081",
+                        "genomad_mini_db_h:md5,1325d5db1da081c479a455a3e7440ae4",
+                        "genomad_mini_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_mini_db_h.index:md5,8c14ed8d3b520be4cd22340a250d26bf",
+                        "genomad_mini_db_mapping:md5,2e10dbb66f99183ff42092777a8089ca",
+                        "genomad_mini_db_taxonomy:md5,5abcff23ab2efa5f5dcfc37cc55ccbbc",
+                        "mini_set_ids:md5,9cc65ecf08bba29cd75e436b18f49e4b",
+                        "names.dmp:md5,83f879df06a69bf16687b5de575ed5ba",
+                        "nodes.dmp:md5,ee4db67cdcf75a5bba6a17b83e57425d",
+                        "plasmid_hallmark_annotation.txt:md5,b4c2568e65b1b8dc9b6f4e506b8ad402",
+                        "version.txt:md5,55a9f2aa32fbd44a46f3b190efa91312",
+                        "virus_hallmark_annotation.txt:md5,351e10e8593afa69d881b7a0128887e9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e98d6885d0b88a7a71f288fcff0b7b14"
+                ],
+                "genomad_db": [
+                    [
+                        [
+                            "version-checkpoint.txt:md5,6527da533ace4cb4473cc907f265f170"
+                        ],
+                        "genomad_db:md5,b9ce17f8b01203c37a9147b5294dace6",
+                        "genomad_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_db.index:md5,5693ab7d5fe2c7947a9a43a9b5705f55",
+                        "genomad_db.lookup:md5,973c8434e0cf70593af1f888c4424876",
+                        "genomad_db.source:md5,6805958c7c99a8e8ab38095a40dc0081",
+                        "genomad_db_h:md5,1325d5db1da081c479a455a3e7440ae4",
+                        "genomad_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_db_h.index:md5,8c14ed8d3b520be4cd22340a250d26bf",
+                        "genomad_db_mapping:md5,2e10dbb66f99183ff42092777a8089ca",
+                        "genomad_db_taxonomy:md5,5abcff23ab2efa5f5dcfc37cc55ccbbc",
+                        "genomad_integrase_db:md5,23e19f271d2d65261588821a1e7d2b30",
+                        "genomad_integrase_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_integrase_db.index:md5,7bae797a783d3f12c75845130ccb9b8a",
+                        "genomad_integrase_db.lookup:md5,cc0702fcafb9a0b27992fd54fc699d25",
+                        "genomad_integrase_db.source:md5,b6ff391f60a2d9d615c7eb41fbf01c19",
+                        "genomad_integrase_db_h:md5,118e59c1b7bbbdfa6776c17da3db430b",
+                        "genomad_integrase_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_integrase_db_h.index:md5,2e8987568dae1a3f4c0207657fd84205",
+                        "genomad_marker_metadata.tsv:md5,fcf64cdbfcd0e099b44143ff99133fed",
+                        "genomad_mini_db:md5,b9ce17f8b01203c37a9147b5294dace6",
+                        "genomad_mini_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828",
+                        "genomad_mini_db.index:md5,e62e3de510ea7f5e73038f51ab02330f",
+                        "genomad_mini_db.lookup:md5,973c8434e0cf70593af1f888c4424876",
+                        "genomad_mini_db.source:md5,6805958c7c99a8e8ab38095a40dc0081",
+                        "genomad_mini_db_h:md5,1325d5db1da081c479a455a3e7440ae4",
+                        "genomad_mini_db_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                        "genomad_mini_db_h.index:md5,8c14ed8d3b520be4cd22340a250d26bf",
+                        "genomad_mini_db_mapping:md5,2e10dbb66f99183ff42092777a8089ca",
+                        "genomad_mini_db_taxonomy:md5,5abcff23ab2efa5f5dcfc37cc55ccbbc",
+                        "mini_set_ids:md5,9cc65ecf08bba29cd75e436b18f49e4b",
+                        "names.dmp:md5,83f879df06a69bf16687b5de575ed5ba",
+                        "nodes.dmp:md5,ee4db67cdcf75a5bba6a17b83e57425d",
+                        "plasmid_hallmark_annotation.txt:md5,b4c2568e65b1b8dc9b6f4e506b8ad402",
+                        "version.txt:md5,55a9f2aa32fbd44a46f3b190efa91312",
+                        "virus_hallmark_annotation.txt:md5,351e10e8593afa69d881b7a0128887e9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e98d6885d0b88a7a71f288fcff0b7b14"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-03T17:38:10.13471002"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genomad/download/tests/nextflow.config b/modules/nf-core/genomad/download/tests/nextflow.config
new file mode 100644
index 00000000000..3ae5aa12459
--- /dev/null
+++ b/modules/nf-core/genomad/download/tests/nextflow.config
@@ -0,0 +1,2 @@
+docker.fixOwnership = false
+docker.runOptions = '-u $(id -u):$(id -g)'
diff --git a/modules/nf-core/genomad/download/tests/tags.yml b/modules/nf-core/genomad/download/tests/tags.yml
new file mode 100644
index 00000000000..27b7acb6e75
--- /dev/null
+++ b/modules/nf-core/genomad/download/tests/tags.yml
@@ -0,0 +1,2 @@
+genomad/download:
+  - "modules/nf-core/genomad/download/**"
diff --git a/modules/nf-core/genomad/endtoend/environment.yml b/modules/nf-core/genomad/endtoend/environment.yml
index 11e50f7945e..6ec4ebe9714 100644
--- a/modules/nf-core/genomad/endtoend/environment.yml
+++ b/modules/nf-core/genomad/endtoend/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::genomad=1.5.2
+  - bioconda::genomad=1.7.4
diff --git a/modules/nf-core/genomad/endtoend/main.nf b/modules/nf-core/genomad/endtoend/main.nf
index 81bb944ae0e..00918a1383d 100644
--- a/modules/nf-core/genomad/endtoend/main.nf
+++ b/modules/nf-core/genomad/endtoend/main.nf
@@ -4,26 +4,26 @@ process GENOMAD_ENDTOEND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genomad:1.7.4--pyhdfd78af_0':
+        'biocontainers/genomad:1.7.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(fasta)
     path  genomad_db
 
     output:
-    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification
+    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification   , optional: true
     tuple val(meta), path("*_annotate/*_taxonomy.tsv")                                      , emit: taxonomy
     tuple val(meta), path("*_find_proviruses/*_provirus.tsv")                               , emit: provirus
     tuple val(meta), path("*_score_calibration/*_compositions.tsv")                         , emit: compositions                , optional: true
     tuple val(meta), path("*_score_calibration/*_calibrated_aggregated_classification.tsv") , emit: calibrated_classification   , optional: true
-    tuple val(meta), path("*_summary/*_plasmid.fna")                                        , emit: plasmid_fasta
+    tuple val(meta), path("*_summary/*_plasmid.fna.gz")                                     , emit: plasmid_fasta
     tuple val(meta), path("*_summary/*_plasmid_genes.tsv")                                  , emit: plasmid_genes
-    tuple val(meta), path("*_summary/*_plasmid_proteins.faa")                               , emit: plasmid_proteins
+    tuple val(meta), path("*_summary/*_plasmid_proteins.faa.gz")                            , emit: plasmid_proteins
     tuple val(meta), path("*_summary/*_plasmid_summary.tsv")                                , emit: plasmid_summary
-    tuple val(meta), path("*_summary/*_virus.fna")                                          , emit: virus_fasta
+    tuple val(meta), path("*_summary/*_virus.fna.gz")                                       , emit: virus_fasta
     tuple val(meta), path("*_summary/*_virus_genes.tsv")                                    , emit: virus_genes
-    tuple val(meta), path("*_summary/*_virus_proteins.faa")                                 , emit: virus_proteins
+    tuple val(meta), path("*_summary/*_virus_proteins.faa.gz")                              , emit: virus_proteins
     tuple val(meta), path("*_summary/*_virus_summary.tsv")                                  , emit: virus_summary
     path "versions.yml"                                                                     , emit: versions
 
@@ -42,6 +42,9 @@ process GENOMAD_ENDTOEND {
         --threads $task.cpus \\
         $args
 
+    gzip ./**/*.fna
+    gzip ./**/*.faa
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         genomad: \$(echo \$(genomad --version 2>&1) | sed 's/^.*geNomad, version //; s/ .*\$//')
@@ -65,13 +68,13 @@ process GENOMAD_ENDTOEND {
     touch ${filename}_score_calibration/${filename}_calibrated_aggregated_classification.tsv
     touch ${filename}_score_calibration/${filename}_compositions.tsv
     mkdir ${filename}_summary
-    touch ${filename}_summary/${filename}_plasmid.fna
+    touch ${filename}_summary/${filename}_plasmid.fna.gz
     touch ${filename}_summary/${filename}_plasmid_genes.tsv
-    touch ${filename}_summary/${filename}_plasmid_proteins.faa
+    touch ${filename}_summary/${filename}_plasmid_proteins.faa.gz
     touch ${filename}_summary/${filename}_plasmid_summary.tsv
-    touch ${filename}_summary/${filename}_virus.fna
+    touch ${filename}_summary/${filename}_virus.fna.gz
     touch ${filename}_summary/${filename}_virus_genes.tsv
-    touch ${filename}_summary/${filename}_virus_proteins.faa
+    touch ${filename}_summary/${filename}_virus_proteins.faa.gz
     touch ${filename}_summary/${filename}_virus_summary.tsv
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/genomad/endtoend/meta.yml b/modules/nf-core/genomad/endtoend/meta.yml
index 8868bfbe2f6..044496cdf1d 100644
--- a/modules/nf-core/genomad/endtoend/meta.yml
+++ b/modules/nf-core/genomad/endtoend/meta.yml
@@ -15,7 +15,7 @@ tools:
       documentation: https://portal.nersc.gov/genomad/
       tool_dev_url: https://github.com/apcamargo/genomad/
       doi: 10.1101/2023.03.05.531206
-      licence: "['Lawrence Berkeley National Labs BSD variant license']"
+      licence: ["Lawrence Berkeley National Labs BSD variant license"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/genomad/endtoend/tests/main.nf.test b/modules/nf-core/genomad/endtoend/tests/main.nf.test
new file mode 100644
index 00000000000..55c6771f9b1
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/main.nf.test
@@ -0,0 +1,83 @@
+nextflow_process {
+
+    name "Test Process GENOMAD_ENDTOEND"
+    script "../main.nf"
+    process "GENOMAD_ENDTOEND"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genomad"
+    tag "genomad/download"
+    tag "genomad/endtoend"
+
+    test("sarscov2 - genome - fasta") {
+        setup {
+            run("GENOMAD_DOWNLOAD") {
+                script "../../download/main.nf"
+                }
+            }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                input[1] = GENOMAD_DOWNLOAD.out.genomad_db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.aggregated_classification,
+                    process.out.taxonomy,
+                    process.out.provirus,
+                    process.out.compositions,
+                    process.out.calibrated_classification,
+                    process.out.plasmid_genes,
+                    process.out.virus_fasta,
+                    process.out.virus_genes,
+                    process.out.virus_proteins,
+                    process.out.virus_summary,
+                    process.out.versions,
+                    ).match()
+                },
+                { assert file(process.out.plasmid_fasta.get(0).get(1)).exists() },
+                { assert file(process.out.plasmid_proteins.get(0).get(1)).exists() }
+            )
+        }
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+
+        setup {
+            run("GENOMAD_DOWNLOAD") {
+                script "../../download/main.nf"
+                }
+            }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                input[1] = GENOMAD_DOWNLOAD.out.genomad_db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap b/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap
new file mode 100644
index 00000000000..00c02faaf08
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/main.nf.test.snap
@@ -0,0 +1,281 @@
+{
+    "sarscov2 - genome - fasta": {
+        "content": [
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                ]
+            ],
+            [
+                "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+            ]
+        ],
+        "timestamp": "2024-01-03T00:05:48.225084591"
+    },
+    "sarscov2 - genome - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                    ]
+                ],
+                "13": [
+                    "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_proteins.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_summary.tsv:md5,8c4ddaa8a90da779c11537be0fddb799"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "aggregated_classification": [
+                    
+                ],
+                "calibrated_classification": [
+                    
+                ],
+                "compositions": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_compositions.tsv:md5,9168bea9fe82a979a698d259e1bb906a"
+                    ]
+                ],
+                "plasmid_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "plasmid_genes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_genes.tsv:md5,55818cae5a57381b77778076e99605e6"
+                    ]
+                ],
+                "plasmid_proteins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_proteins.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "plasmid_summary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_plasmid_summary.tsv:md5,8c4ddaa8a90da779c11537be0fddb799"
+                    ]
+                ],
+                "provirus": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_provirus.tsv:md5,93a6bca59b0bf7f57c0b9b60d2e57082"
+                    ]
+                ],
+                "taxonomy": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_taxonomy.tsv:md5,44c6cf5ff4c836f66648457ae8deb0d5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,cebe18512f616530fff490a64e595cb6"
+                ],
+                "virus_fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus.fna.gz:md5,483f4a5dfe60171c86ee9b7e6dff908b"
+                    ]
+                ],
+                "virus_genes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_genes.tsv:md5,f84d8a9fce3c92c49e78672bea16561f"
+                    ]
+                ],
+                "virus_proteins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_proteins.faa.gz:md5,6850bd46dcb921e5cfb23bfbb8fcc12b"
+                    ]
+                ],
+                "virus_summary": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome_virus_summary.tsv:md5,8cbcf95c2ab397da26b6dca8014e86f4"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2024-01-03T00:07:52.60021527"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/genomad/endtoend/tests/nextflow.config b/modules/nf-core/genomad/endtoend/tests/nextflow.config
new file mode 100644
index 00000000000..149f4a4f819
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GENOMAD_ENDTOEND {
+        ext.args = '--splits 6 --enable-score-calibration --sensitivity 0.1 --disable-nn-classification'
+    }
+}
diff --git a/modules/nf-core/genomad/endtoend/tests/tags.yml b/modules/nf-core/genomad/endtoend/tests/tags.yml
new file mode 100644
index 00000000000..497ed727ba3
--- /dev/null
+++ b/modules/nf-core/genomad/endtoend/tests/tags.yml
@@ -0,0 +1,2 @@
+genomad/endtoend:
+  - "modules/nf-core/genomad/endtoend/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index d37a2629232..3dab96d77b1 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -975,12 +975,6 @@ genmod/models:
 genmod/score:
   - modules/nf-core/genmod/score/**
   - tests/modules/nf-core/genmod/score/**
-genomad/download:
-  - modules/nf-core/genomad/download/**
-  - tests/modules/nf-core/genomad/download/**
-genomad/endtoend:
-  - modules/nf-core/genomad/endtoend/**
-  - tests/modules/nf-core/genomad/endtoend/**
 genomescope2:
   - modules/nf-core/genomescope2/**
   - tests/modules/nf-core/genomescope2/**
diff --git a/tests/modules/nf-core/genomad/download/main.nf b/tests/modules/nf-core/genomad/download/main.nf
deleted file mode 100644
index c14b1003d32..00000000000
--- a/tests/modules/nf-core/genomad/download/main.nf
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENOMAD_DOWNLOAD } from '../../../../../modules/nf-core/genomad/download/main.nf'
-
-workflow test_genomad_download {
-
-    GENOMAD_DOWNLOAD ( )
-}
diff --git a/tests/modules/nf-core/genomad/download/nextflow.config b/tests/modules/nf-core/genomad/download/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/genomad/download/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/genomad/download/test.yml b/tests/modules/nf-core/genomad/download/test.yml
deleted file mode 100644
index f134e5055b5..00000000000
--- a/tests/modules/nf-core/genomad/download/test.yml
+++ /dev/null
@@ -1,120 +0,0 @@
-- name: genomad download test_genomad_download
-  command: nextflow run ./tests/modules/nf-core/genomad/download -entry test_genomad_download -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genomad/download/nextflow.config
-  tags:
-    - genomad
-    - genomad/download
-  files:
-    - path: output/genomad/genomad_db/genomad_db
-      md5sum: b9ce17f8b01203c37a9147b5294dace6
-    - path: output/genomad/genomad_db/genomad_db.dbtype
-      md5sum: f2dd0dedb2c260419ece4a9e03b2e828
-    - path: output/genomad/genomad_db/genomad_db.index
-      md5sum: 5693ab7d5fe2c7947a9a43a9b5705f55
-    - path: output/genomad/genomad_db/genomad_db.lookup
-      md5sum: 973c8434e0cf70593af1f888c4424876
-    - path: output/genomad/genomad_db/genomad_db.source
-      md5sum: 6805958c7c99a8e8ab38095a40dc0081
-    - path: output/genomad/genomad_db/genomad_db_h
-      md5sum: 1325d5db1da081c479a455a3e7440ae4
-    - path: output/genomad/genomad_db/genomad_db_h.dbtype
-      md5sum: 740bab4f9ec8808aedb68d6b1281aeb2
-    - path: output/genomad/genomad_db/genomad_db_h.index
-      md5sum: 8c14ed8d3b520be4cd22340a250d26bf
-    - path: output/genomad/genomad_db/genomad_db_mapping
-      md5sum: e56fa490b1050a8a3e82119976918e60
-    - path: output/genomad/genomad_db/genomad_db_taxonomy
-      md5sum: bf46bbcd28214cb34aa9ef6c891b7114
-    - path: output/genomad/genomad_db/genomad_integrase_db
-      md5sum: 23e19f271d2d65261588821a1e7d2b30
-    - path: output/genomad/genomad_db/genomad_integrase_db.dbtype
-      md5sum: f2dd0dedb2c260419ece4a9e03b2e828
-    - path: output/genomad/genomad_db/genomad_integrase_db.index
-      md5sum: 7bae797a783d3f12c75845130ccb9b8a
-    - path: output/genomad/genomad_db/genomad_integrase_db.lookup
-      md5sum: cc0702fcafb9a0b27992fd54fc699d25
-    - path: output/genomad/genomad_db/genomad_integrase_db.source
-      md5sum: b6ff391f60a2d9d615c7eb41fbf01c19
-    - path: output/genomad/genomad_db/genomad_integrase_db_h
-      md5sum: 118e59c1b7bbbdfa6776c17da3db430b
-    - path: output/genomad/genomad_db/genomad_integrase_db_h.dbtype
-      md5sum: 740bab4f9ec8808aedb68d6b1281aeb2
-    - path: output/genomad/genomad_db/genomad_integrase_db_h.index
-      md5sum: 2e8987568dae1a3f4c0207657fd84205
-    - path: output/genomad/genomad_db/genomad_marker_metadata.tsv
-      md5sum: e7f98a16fee1e71498384ca9b2492eeb
-    - path: output/genomad/genomad_db/genomad_mini_db
-      md5sum: b9ce17f8b01203c37a9147b5294dace6
-    - path: output/genomad/genomad_db/genomad_mini_db.dbtype
-      md5sum: f2dd0dedb2c260419ece4a9e03b2e828
-    - path: output/genomad/genomad_db/genomad_mini_db.index
-      md5sum: e62e3de510ea7f5e73038f51ab02330f
-    - path: output/genomad/genomad_db/genomad_mini_db.lookup
-      md5sum: 973c8434e0cf70593af1f888c4424876
-    - path: output/genomad/genomad_db/genomad_mini_db.source
-      md5sum: 6805958c7c99a8e8ab38095a40dc0081
-    - path: output/genomad/genomad_db/genomad_mini_db_h
-      md5sum: 1325d5db1da081c479a455a3e7440ae4
-    - path: output/genomad/genomad_db/genomad_mini_db_h.dbtype
-      md5sum: 740bab4f9ec8808aedb68d6b1281aeb2
-    - path: output/genomad/genomad_db/genomad_mini_db_h.index
-      md5sum: 8c14ed8d3b520be4cd22340a250d26bf
-    - path: output/genomad/genomad_db/genomad_mini_db_mapping
-      md5sum: e56fa490b1050a8a3e82119976918e60
-    - path: output/genomad/genomad_db/genomad_mini_db_taxonomy
-      md5sum: bf46bbcd28214cb34aa9ef6c891b7114
-    - path: output/genomad/genomad_db/mini_set_ids
-      md5sum: 9cc65ecf08bba29cd75e436b18f49e4b
-    - path: output/genomad/genomad_db/names.dmp
-      md5sum: 83f879df06a69bf16687b5de575ed5ba
-    - path: output/genomad/genomad_db/nodes.dmp
-      md5sum: ee4db67cdcf75a5bba6a17b83e57425d
-    - path: output/genomad/genomad_db/plasmid_hallmark_annotation.txt
-      md5sum: 36bbd98d2f9e2f7abad5ef31aca1ce0c
-    - path: output/genomad/genomad_db/version.txt
-      md5sum: 84b17206d983a7430710b2a1f8ae52b8
-    - path: output/genomad/genomad_db/virus_hallmark_annotation.txt
-      md5sum: 5211d849ade305ab989472a82c206700
-    - path: output/genomad/versions.yml
-
-- name: genomad download test_genomad_download_stub
-  command: nextflow run ./tests/modules/nf-core/genomad/download -entry test_genomad_download -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genomad/download/nextflow.config -stub-run
-  tags:
-    - genomad
-    - genomad/download
-  files:
-    - path: output/genomad/genomad_db/genomad_db
-    - path: output/genomad/genomad_db/genomad_db.dbtype
-    - path: output/genomad/genomad_db/genomad_db.index
-    - path: output/genomad/genomad_db/genomad_db.lookup
-    - path: output/genomad/genomad_db/genomad_db.source
-    - path: output/genomad/genomad_db/genomad_db_h
-    - path: output/genomad/genomad_db/genomad_db_h.dbtype
-    - path: output/genomad/genomad_db/genomad_db_h.index
-    - path: output/genomad/genomad_db/genomad_db_mapping
-    - path: output/genomad/genomad_db/genomad_db_taxonomy
-    - path: output/genomad/genomad_db/genomad_integrase_db
-    - path: output/genomad/genomad_db/genomad_integrase_db.dbtype
-    - path: output/genomad/genomad_db/genomad_integrase_db.index
-    - path: output/genomad/genomad_db/genomad_integrase_db.lookup
-    - path: output/genomad/genomad_db/genomad_integrase_db.source
-    - path: output/genomad/genomad_db/genomad_integrase_db_h
-    - path: output/genomad/genomad_db/genomad_integrase_db_h.dbtype
-    - path: output/genomad/genomad_db/genomad_integrase_db_h.index
-    - path: output/genomad/genomad_db/genomad_marker_metadata.tsv
-    - path: output/genomad/genomad_db/genomad_mini_db
-    - path: output/genomad/genomad_db/genomad_mini_db.dbtype
-    - path: output/genomad/genomad_db/genomad_mini_db.index
-    - path: output/genomad/genomad_db/genomad_mini_db.lookup
-    - path: output/genomad/genomad_db/genomad_mini_db.source
-    - path: output/genomad/genomad_db/genomad_mini_db_h
-    - path: output/genomad/genomad_db/genomad_mini_db_h.dbtype
-    - path: output/genomad/genomad_db/genomad_mini_db_h.index
-    - path: output/genomad/genomad_db/genomad_mini_db_mapping
-    - path: output/genomad/genomad_db/genomad_mini_db_taxonomy
-    - path: output/genomad/genomad_db/mini_set_ids
-    - path: output/genomad/genomad_db/names.dmp
-    - path: output/genomad/genomad_db/nodes.dmp
-    - path: output/genomad/genomad_db/plasmid_hallmark_annotation.txt
-    - path: output/genomad/genomad_db/version.txt
-    - path: output/genomad/genomad_db/virus_hallmark_annotation.txt
-    - path: output/genomad/versions.yml
diff --git a/tests/modules/nf-core/genomad/endtoend/main.nf b/tests/modules/nf-core/genomad/endtoend/main.nf
deleted file mode 100644
index 7fe54484cc0..00000000000
--- a/tests/modules/nf-core/genomad/endtoend/main.nf
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GENOMAD_DOWNLOAD } from '../../../../../modules/nf-core/genomad/download/main.nf'
-include { GENOMAD_ENDTOEND } from '../../../../../modules/nf-core/genomad/endtoend/main.nf'
-
-workflow test_genomad_endtoend {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
-    ]
-
-    GENOMAD_DOWNLOAD ( )
-
-    GENOMAD_ENDTOEND ( input, GENOMAD_DOWNLOAD.out.genomad_db )
-
-}
diff --git a/tests/modules/nf-core/genomad/endtoend/nextflow.config b/tests/modules/nf-core/genomad/endtoend/nextflow.config
deleted file mode 100644
index f14d04170f2..00000000000
--- a/tests/modules/nf-core/genomad/endtoend/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: GENOMAD_ENDTOEND {
-        ext.args = '--splits 6 --enable-score-calibration'
-    }
-}
diff --git a/tests/modules/nf-core/genomad/endtoend/test.yml b/tests/modules/nf-core/genomad/endtoend/test.yml
deleted file mode 100644
index db99b81bb7a..00000000000
--- a/tests/modules/nf-core/genomad/endtoend/test.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-- name: genomad endtoend test_genomad_endtoend
-  command: nextflow run ./tests/modules/nf-core/genomad/endtoend -entry test_genomad_endtoend -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genomad/endtoend/nextflow.config
-  tags:
-    - genomad
-    - genomad/endtoend
-  files:
-    - path: output/genomad/scaffolds_aggregated_classification/scaffolds_aggregated_classification.tsv
-      md5sum: cb1429d7f21235e86a85a7ee64b1c447
-    - path: output/genomad/scaffolds_annotate/scaffolds_taxonomy.tsv
-      md5sum: a43a36aa68f9cb87a2221381d106c6e0
-    - path: output/genomad/scaffolds_find_proviruses/scaffolds_provirus.tsv
-      md5sum: 93a6bca59b0bf7f57c0b9b60d2e57082
-    - path: output/genomad/scaffolds_score_calibration/scaffolds_calibrated_aggregated_classification.tsv
-      md5sum: bf35570c88a4bf39a3b90424062911bd
-    - path: output/genomad/scaffolds_score_calibration/scaffolds_compositions.tsv
-      md5sum: 9168bea9fe82a979a698d259e1bb906a
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid.fna
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_genes.tsv
-      md5sum: 55818cae5a57381b77778076e99605e6
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_proteins.faa
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_summary.tsv
-      md5sum: 8c4ddaa8a90da779c11537be0fddb799
-    - path: output/genomad/scaffolds_summary/scaffolds_virus.fna
-      md5sum: 430784780f04e095a9fee7613e030052
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_genes.tsv
-      md5sum: 13e72216197de1c6e46bca01eb585eda
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_proteins.faa
-      md5sum: 13526a60bf0149b8d48e5ff68190e5d4
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_summary.tsv
-      md5sum: ec7b0da75d18b25a18494b5d66c89ef8
-    - path: output/genomad/versions.yml
-
-- name: genomad endtoend test_genomad_endtoend_stub
-  command: nextflow run ./tests/modules/nf-core/genomad/endtoend -entry test_genomad_endtoend -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/genomad/endtoend/nextflow.config -stub-run
-  tags:
-    - genomad
-    - genomad/endtoend
-  files:
-    - path: output/genomad/scaffolds_aggregated_classification/scaffolds_aggregated_classification.tsv
-    - path: output/genomad/scaffolds_annotate/scaffolds_taxonomy.tsv
-    - path: output/genomad/scaffolds_find_proviruses/scaffolds_provirus.tsv
-    - path: output/genomad/scaffolds_score_calibration/scaffolds_calibrated_aggregated_classification.tsv
-    - path: output/genomad/scaffolds_score_calibration/scaffolds_compositions.tsv
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid.fna
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_genes.tsv
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_proteins.faa
-    - path: output/genomad/scaffolds_summary/scaffolds_plasmid_summary.tsv
-    - path: output/genomad/scaffolds_summary/scaffolds_virus.fna
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_genes.tsv
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_proteins.faa
-    - path: output/genomad/scaffolds_summary/scaffolds_virus_summary.tsv
-    - path: output/genomad/versions.yml