diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9d257bf1d4..f7e5a8788c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 
 ### Linting
 
+- linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
 
 ### Modules
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index cffabe6c3f..7970c34081 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -600,7 +600,7 @@ def lint(
 
     # Run the lint tests!
     try:
-        lint_obj, module_lint_obj = run_linting(
+        lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(
             dir,
             release,
             fix,
@@ -613,7 +613,10 @@ def lint(
             json,
             ctx.obj["hide_progress"],
         )
-        if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
+        swf_failed = 0
+        if subworkflow_lint_obj is not None:
+            swf_failed = len(subworkflow_lint_obj.failed)
+        if len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
index 797ebbcc91..b4d0c10ff3 100644
--- a/nf_core/lint/__init__.py
+++ b/nf_core/lint/__init__.py
@@ -20,6 +20,7 @@
 
 import nf_core.lint_utils
 import nf_core.modules.lint
+import nf_core.subworkflows.lint
 import nf_core.utils
 from nf_core import __version__
 from nf_core.lint_utils import console
@@ -53,6 +54,8 @@ def run_linting(
 
     Returns:
         An object of type :class:`PipelineLint` that contains all the linting results.
+        An object of type :class:`ComponentLint` that contains all the linting results for the modules.
+        An object of type :class:`ComponentLint` that contains all the linting results for the subworkflows.
     """
 
     # Verify that the requested tests exist
@@ -87,6 +90,11 @@ def run_linting(
 
     # Create the modules lint object
     module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_progress)
+    # Create the subworkflows lint object
+    try:
+        subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, hide_progress=hide_progress)
+    except LookupError:
+        subworkflow_lint_obj = None
 
     # Verify that the pipeline is correctly configured and has  a modules.json file
     module_lint_obj.has_valid_directory()
@@ -98,10 +106,19 @@ def run_linting(
         module_lint_tests = list(
             set(key).intersection(set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)))
         )
+        # Select only the subworkflow lint tests
+        subworkflow_lint_tests = list(
+            set(key).intersection(
+                set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True))
+            )
+        )
     else:
         # If no key is supplied, run the default modules tests
         module_lint_tests = ("module_changes", "module_version")
+        subworkflow_lint_tests = ("subworkflow_changes", "subworkflow_version")
     module_lint_obj.filter_tests_by_key(module_lint_tests)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
 
     # Set up files for modules linting test
     module_lint_obj.set_up_pipeline_files()
@@ -119,11 +136,19 @@ def run_linting(
         module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=True)
     if len(module_lint_obj.all_remote_components) > 0:
         module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=False)
+    # Run the subworkflows lint tests
+    if subworkflow_lint_obj is not None:
+        if len(subworkflow_lint_obj.all_local_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_local_components, local=True)
+        if len(subworkflow_lint_obj.all_remote_components) > 0:
+            subworkflow_lint_obj.lint_subworkflows(subworkflow_lint_obj.all_remote_components, local=False)
 
     # Print the results
     lint_obj._print_results(show_passed)
     module_lint_obj._print_results(show_passed, sort_by=sort_by)
-    nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj)
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj._print_results(show_passed, sort_by=sort_by)
+    nf_core.lint_utils.print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj)
     nf_core.lint_utils.print_fixes(lint_obj)
 
     # Save results to Markdown file
@@ -142,7 +167,7 @@ def run_linting(
         if release_mode:
             log.info("Reminder: Lint tests were run in --release mode.")
 
-    return lint_obj, module_lint_obj
+    return lint_obj, module_lint_obj, subworkflow_lint_obj
 
 
 class PipelineLint(nf_core.utils.Pipeline):
diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
index c2fd75d375..6eca6522d4 100644
--- a/nf_core/lint_utils.py
+++ b/nf_core/lint_utils.py
@@ -16,13 +16,20 @@
 console = Console(force_terminal=nf_core.utils.rich_force_colors())
 
 
-def print_joint_summary(lint_obj, module_lint_obj):
-    """Print a joint summary of the general pipe lint tests and the module lint tests"""
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed)
+def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
+    """Print a joint summary of the general pipe lint tests and the module and subworkflow lint tests"""
+    swf_passed = 0
+    swf_warned = 0
+    swf_failed = 0
+    if subworkflow_lint_obj is not None:
+        swf_passed = len(subworkflow_lint_obj.passed)
+        swf_warned = len(subworkflow_lint_obj.warned)
+        swf_failed = len(subworkflow_lint_obj.failed)
+    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + swf_passed
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
-    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned)
-    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed)
+    nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + swf_warned
+    nbr_failed = len(lint_obj.failed) + len(module_lint_obj.failed) + swf_failed
 
     summary_colour = "red" if nbr_failed > 0 else "green"
     table = Table(box=rich.box.ROUNDED, style=summary_colour)
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 223bcacc9c..8660da2d42 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
+                        "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
index f0c63f6984..9b3272bc11 100644
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.17
+  - bioconda::multiqc=1.19
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 7685b33cde..f2187611cc 100644
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.17--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
index eec1db10a2..b1e1630bb3 100644
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
@@ -31,7 +31,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    file(process.out.mqc_yml[0]).readLines()[0..10],
+                    file(process.out.yml[0]).readLines()[0..7]
+                    ).match()
+                }
             )
         }
     }
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
index 4274ed57aa..5f59a936d7 100644
--- a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
+++ b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
@@ -1,27 +1,33 @@
 {
     "Should run without failures": {
         "content": [
-            {
-                "0": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ],
-                "1": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "2": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "mqc_yml": [
-                    "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d"
-                ],
-                "versions": [
-                    "versions.yml:md5,3843ac526e762117eedf8825b40683df"
-                ],
-                "yml": [
-                    "software_versions.yml:md5,1c851188476409cda5752ce971b20b58"
-                ]
-            }
+            [
+                "versions.yml:md5,76d454d92244589d32455833f7c1ba6d"
+            ],
+            [
+                "data: \"<style>\\n#nf-core-versions tbody:nth-child(even) {\\n    background-color: #f2f2f2;\\n\\",
+                "  }\\n</style>\\n<table class=\\\"table\\\" style=\\\"width:100%\\\" id=\\\"nf-core-versions\\\"\\",
+                "  >\\n    <thead>\\n        <tr>\\n            <th> Process Name </th>\\n            <th>\\",
+                "  \\ Software </th>\\n            <th> Version  </th>\\n        </tr>\\n    </thead>\\n\\",
+                "  \\n<tbody>\\n<tr>\\n    <td><samp>CUSTOM_DUMPSOFTWAREVERSIONS</samp></td>\\n    <td><samp>python</samp></td>\\n\\",
+                "  \\    <td><samp>3.11.7</samp></td>\\n</tr>\\n\\n<tr>\\n    <td><samp></samp></td>\\n \\",
+                "  \\   <td><samp>yaml</samp></td>\\n    <td><samp>5.4.1</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>TOOL1</samp></td>\\n    <td><samp>tool1</samp></td>\\n\\",
+                "  \\    <td><samp>0.11.9</samp></td>\\n</tr>\\n\\n</tbody>\\n<tbody>\\n<tr>\\n    <td><samp>TOOL2</samp></td>\\n\\",
+                "  \\    <td><samp>tool2</samp></td>\\n    <td><samp>1.9</samp></td>\\n</tr>\\n\\n</tbody>\\n\\",
+                "  <tbody>\\n<tr>\\n    <td><samp>Workflow</samp></td>\\n    <td><samp>Nextflow</samp></td>\\n\\"
+            ],
+            [
+                "CUSTOM_DUMPSOFTWAREVERSIONS:",
+                "  python: 3.11.7",
+                "  yaml: 5.4.1",
+                "TOOL1:",
+                "  tool1: 0.11.9",
+                "TOOL2:",
+                "  tool2: '1.9'",
+                "Workflow:"
+            ]
         ],
-        "timestamp": "2023-11-03T14:43:22.157011"
+        "timestamp": "2024-01-09T23:01:18.710682"
     }
-}
+}
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test
index b9e8f926eb..1f21c66469 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test
@@ -3,24 +3,20 @@ nextflow_process {
     name "Test Process FASTQC"
     script "../main.nf"
     process "FASTQC"
+
     tag "modules"
     tag "modules_nfcore"
     tag "fastqc"
 
-    test("Single-Read") {
+    test("sarscov2 single-end [fastq]") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id: 'test', single_end:true ],
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
                 """
             }
         }
@@ -28,82 +24,189 @@ nextflow_process {
         then {
             assertAll (
             { assert process.success },
+
             // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
             // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
             // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
-            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert snapshot(process.out.versions).match("versions") },
-            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
+                ])
+            """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
             )
         }
     }
-// TODO
-// //
-// // Test with paired-end data
-// //
-// workflow test_fastqc_paired_end {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 [
-//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
-//                 ]
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with interleaved data
-// //
-// workflow test_fastqc_interleaved {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with bam data
-// //
-// workflow test_fastqc_bam {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with multiple samples
-// //
-// workflow test_fastqc_multiple {
-//     input = [
-//                 [id: 'test', single_end: false], // meta map
-//                 [
-//                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
-//                     file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true)
-//                 ]
-//             ]
-
-//     FASTQC ( input )
-// }
-
-// //
-// // Test with custom prefix
-// //
-// workflow test_fastqc_custom_prefix {
-//     input = [
-//                 [ id:'mysample', single_end:true ], // meta map
-//                 file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-//             ]
-
-//     FASTQC ( input )
-// }
+
+    test("sarscov2 paired-end [bam]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: false], // meta map
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
+            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
+            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
+            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
+            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
+            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
+            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
+            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
+            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'mysample', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+
+            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
+            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
+            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+
+            { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastq] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id: 'test', single_end:true ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
+                                process.out.zip.collect { file(it[1]).getName() } +
+                                process.out.versions ).match() }
+            )
+        }
+    }
+
 }
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap
index 636a32cead..5d624bb82e 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -1,10 +1,20 @@
 {
+    "sarscov2 single-end [fastq] - stub": {
+        "content": [
+            [
+                "test.html",
+                "test.zip",
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "timestamp": "2024-01-17T18:40:57.254299"
+    },
     "versions": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
-        "timestamp": "2023-10-09T23:40:54+0000"
+        "timestamp": "2024-01-17T18:36:50.033627"
     }
 }
\ No newline at end of file
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
index bc0bdb5b68..7625b75206 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.18
+  - bioconda::multiqc=1.19
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
index 00cc48d275..1b9f7c431d 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.18--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.19--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
@@ -43,7 +43,7 @@ process MULTIQC {
 
     stub:
     """
-    touch multiqc_data
+    mkdir multiqc_data
     touch multiqc_plots
     touch multiqc_report.html
 
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
index f1aa660eb7..45a9bc35e1 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: multiqc
 description: Aggregate results from bioinformatics analyses across many samples into a single report
 keywords:
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test
index c2dad217c4..d0438eda6b 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test
@@ -7,12 +7,9 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
-    test("MULTIQC: FASTQC") {
+    test("sarscov2 single-end [fastqc]") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             process {
                 """
                 input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
@@ -26,20 +23,17 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.report.get(0)).exists() },
-                { assert path(process.out.data.get(0)).exists() },
-                { assert path(process.out.versions.get(0)).getText().contains("multiqc") }
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("versions") }
             )
         }
 
     }
 
-    test("MULTIQC: FASTQC and a config file") {
+    test("sarscov2 single-end [fastqc] [config]") {
 
         when {
-            params {
-                outdir = "$outputDir"
-            }
             process {
                 """
                 input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
@@ -53,9 +47,35 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.report.get(0)).exists() },
-                { assert path(process.out.data.get(0)).exists() },
-                { assert path(process.out.versions.get(0)).getText().contains("multiqc") }
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.report.collect { file(it).getName() } +
+                                process.out.data.collect { file(it).getName() } +
+                                process.out.plots.collect { file(it).getName() } +
+                                process.out.versions ).match() }
             )
         }
 
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
new file mode 100644
index 0000000000..d37e73040d
--- /dev/null
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -0,0 +1,21 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
+            ]
+        ],
+        "timestamp": "2024-01-09T23:02:49.911994"
+    },
+    "sarscov2 single-end [fastqc] - stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d"
+            ]
+        ],
+        "timestamp": "2024-01-09T23:03:14.524346"
+    }
+}
\ No newline at end of file
diff --git a/tests/test_cli.py b/tests/test_cli.py
index abb4fba87d..1261e3a9e9 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -263,9 +263,10 @@ def test_create(self, mock_create):
     @mock.patch("nf_core.lint.run_linting")
     def test_lint(self, mock_lint, mock_is_pipeline):
         """Test nf-core lint"""
-        mock_lint_results = (mock.MagicMock, mock.MagicMock)
+        mock_lint_results = (mock.MagicMock, mock.MagicMock, mock.MagicMock)
         mock_lint_results[0].failed = []
         mock_lint_results[1].failed = []
+        mock_lint_results[2].failed = []
         mock_lint.return_value = mock_lint_results
 
         temp_pipeline_dir = tempfile.NamedTemporaryFile()