diff --git a/CHANGELOG.md b/CHANGELOG.md
index 68399a9c0b..30bd00b5c4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -67,6 +67,7 @@
 - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
 - Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
 - Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115))
+- Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077))
 
 ### General
 
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 3f17221056..c7e927c8c8 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1479,11 +1479,14 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
     help="Sort lint output by subworkflow or test name.",
     show_default=True,
 )
-def command_subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by):
+@click.option("--fix", is_flag=True, help="Fix all linting tests if possible.")
+def command_subworkflows_lint(
+    ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by, fix
+):
     """
     Lint one or more subworkflows in a directory.
     """
-    subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by)
+    subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by, fix)
 
 
 # nf-core subworkflows info
diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py
index a32f8d5c3e..8e90a8116b 100644
--- a/nf_core/commands_subworkflows.py
+++ b/nf_core/commands_subworkflows.py
@@ -104,7 +104,7 @@ def subworkflows_list_local(ctx, keywords, json, directory):  # pylint: disable=
         sys.exit(1)
 
 
-def subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by):
+def subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warned, local, passed, sort_by, fix):
     """
     Lint one or more subworkflows in a directory.
 
@@ -121,6 +121,7 @@ def subworkflows_lint(ctx, subworkflow, directory, registry, key, all, fail_warn
         subworkflow_lint = SubworkflowLint(
             directory,
             fail_warned=fail_warned,
+            fix=fix,
             registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
index 98f8be5272..f3e5bf617c 100644
--- a/nf_core/components/info.py
+++ b/nf_core/components/info.py
@@ -229,6 +229,25 @@ def get_remote_yaml(self) -> Optional[dict]:
         self.remote_location = self.modules_repo.remote_url
         return yaml.safe_load(file_contents)
 
+    def generate_params_table(self, type) -> Table:
+        "Generate a rich table for inputs and outputs"
+        table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0)
+        table.add_column(f":inbox_tray: {type}")
+        table.add_column("Description")
+        if self.component_type == "modules":
+            table.add_column("Pattern", justify="right", style="green")
+        elif self.component_type == "subworkflows":
+            table.add_column("Structure", justify="right", style="green")
+        return table
+
+    def get_channel_structure(self, structure: dict) -> str:
+        "Get the structure of a channel"
+        structure_str = ""
+        for key, info in structure.items():
+            pattern = f" - {info['pattern']}" if info.get("pattern") else ""
+            structure_str += f"{key} ({info['type']}{pattern})"
+        return structure_str
+
     def generate_component_info_help(self):
         """Take the parsed meta.yml and generate rich help.
 
@@ -277,33 +296,48 @@ def generate_component_info_help(self):
 
         # Inputs
         if self.meta.get("input"):
-            inputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0)
-            inputs_table.add_column(":inbox_tray: Inputs")
-            inputs_table.add_column("Description")
-            inputs_table.add_column("Pattern", justify="right", style="green")
-            for input in self.meta["input"]:
-                for key, info in input.items():
-                    inputs_table.add_row(
-                        f"[orange1 on black] {key} [/][dim i] ({info['type']})",
-                        Markdown(info["description"] if info["description"] else ""),
-                        info.get("pattern", ""),
-                    )
+            inputs_table = self.generate_params_table("Inputs")
+            for i, input in enumerate(self.meta["input"]):
+                inputs_table.add_row(f"[italic]input[{i}][/]", "", "")
+                if self.component_type == "modules":
+                    for element in input:
+                        for key, info in element.items():
+                            inputs_table.add_row(
+                                f"[orange1 on black] {key} [/][dim i] ({info['type']})",
+                                Markdown(info["description"] if info["description"] else ""),
+                                info.get("pattern", ""),
+                            )
+                elif self.component_type == "subworkflows":
+                    for key, info in input.items():
+                        inputs_table.add_row(
+                            f"[orange1 on black] {key} [/][dim i]",
+                            Markdown(info["description"] if info["description"] else ""),
+                            self.get_channel_structure(info["structure"]) if info.get("structure") else "",
+                        )
 
             renderables.append(inputs_table)
 
         # Outputs
         if self.meta.get("output"):
-            outputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0)
-            outputs_table.add_column(":outbox_tray: Outputs")
-            outputs_table.add_column("Description")
-            outputs_table.add_column("Pattern", justify="right", style="green")
+            outputs_table = self.generate_params_table("Outputs")
             for output in self.meta["output"]:
-                for key, info in output.items():
-                    outputs_table.add_row(
-                        f"[orange1 on black] {key} [/][dim i] ({info['type']})",
-                        Markdown(info["description"] if info["description"] else ""),
-                        info.get("pattern", ""),
-                    )
+                if self.component_type == "modules":
+                    for ch_name, elements in output.items():
+                        outputs_table.add_row(f"{ch_name}", "", "")
+                        for element in elements:
+                            for key, info in element.items():
+                                outputs_table.add_row(
+                                    f"[orange1 on black] {key} [/][dim i] ({info['type']})",
+                                    Markdown(info["description"] if info["description"] else ""),
+                                    info.get("pattern", ""),
+                                )
+                elif self.component_type == "subworkflows":
+                    for key, info in output.items():
+                        outputs_table.add_row(
+                            f"[orange1 on black] {key} [/][dim i]",
+                            Markdown(info["description"] if info["description"] else ""),
+                            self.get_channel_structure(info["structure"]) if info.get("structure") else "",
+                        )
 
             renderables.append(outputs_table)
 
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 84c9a651ed..9cce94acb5 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -5,7 +5,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import List, Optional, Tuple, Union
+from typing import Any, List, Optional, Tuple, Union
 
 log = logging.getLogger(__name__)
 
@@ -41,6 +41,7 @@ def __init__(
             remote_component (bool): Whether the module is to be treated as a
                                      nf-core or local component
         """
+        self.component_type = component_type
         self.component_name = component_name
         self.repo_url = repo_url
         self.component_dir = component_dir
@@ -170,65 +171,95 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
 
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
-        inputs: list[list[dict[str, dict[str, str]]]] = []
+        inputs: Any = []  # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]'
         with open(self.main_nf) as f:
             data = f.read()
-        # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
-        # regex matches:
-        # val(foo)
-        # path(bar)
-        # val foo
-        # val bar
-        # path bar
-        # path foo
-        # don't match anything inside comments or after "output:"
-        if "input:" not in data:
-            log.debug(f"Could not find any inputs in {self.main_nf}")
-            return
-        input_data = data.split("input:")[1].split("output:")[0]
-        for line in input_data.split("\n"):
-            channel_elements: list[dict[str, dict[str, str]]] = []
-            regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
-            matches = re.finditer(regex, line)
-            for _, match in enumerate(matches, start=1):
-                input_val = None
-                if match.group(3):
-                    input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
-                elif match.group(4):
-                    input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
-                if input_val:
-                    channel_elements.append({input_val: {}})
-            if len(channel_elements) > 0:
-                inputs.append(channel_elements)
-        log.debug(f"Found {len(inputs)} inputs in {self.main_nf}")
-        self.inputs = inputs
+        if self.component_type == "modules":
+            # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo
+            # regex matches:
+            # val(foo)
+            # path(bar)
+            # val foo
+            # val bar
+            # path bar
+            # path foo
+            # don't match anything inside comments or after "output:"
+            if "input:" not in data:
+                log.debug(f"Could not find any inputs in {self.main_nf}")
+                return
+            input_data = data.split("input:")[1].split("output:")[0]
+            for line in input_data.split("\n"):
+                channel_elements: Any = []
+                regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+                matches = re.finditer(regex, line)
+                for _, match in enumerate(matches, start=1):
+                    input_val = None
+                    if match.group(3):
+                        input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                    elif match.group(4):
+                        input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                    if input_val:
+                        channel_elements.append({input_val: {}})
+                if len(channel_elements) > 0:
+                    inputs.append(channel_elements)
+            log.debug(f"Found {len(inputs)} inputs in {self.main_nf}")
+            self.inputs = inputs
+        elif self.component_type == "subworkflows":
+            # get input values from main.nf after "take:"
+            if "take:" not in data:
+                log.debug(f"Could not find any inputs in {self.main_nf}")
+                return
+            # get all lines between "take" and "main" or "emit"
+            input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0]
+            for line in input_data.split("\n"):
+                try:
+                    inputs.append(line.split()[0])
+                except IndexError:
+                    pass  # Empty lines
+            log.debug(f"Found {len(inputs)} inputs in {self.main_nf}")
+            self.inputs = inputs
 
     def get_outputs_from_main_nf(self):
         outputs = []
         with open(self.main_nf) as f:
             data = f.read()
-        # get output values from main.nf after "output:". the names are always after "emit:"
-        if "output:" not in data:
-            log.debug(f"Could not find any outputs in {self.main_nf}")
-            return outputs
-        output_data = data.split("output:")[1].split("when:")[0]
-        regex_emit = r"emit:\s*([^)\s,]+)"
-        regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
-        for line in output_data.split("\n"):
-            match_emit = re.search(regex_emit, line)
-            matches_elements = re.finditer(regex_elements, line)
-            if not match_emit:
-                continue
-            output_channel = {match_emit.group(1): []}
-            for _, match_element in enumerate(matches_elements, start=1):
-                output_val = None
-                if match_element.group(3):
-                    output_val = match_element.group(3)
-                elif match_element.group(4):
-                    output_val = match_element.group(4)
-                if output_val:
-                    output_val = output_val.strip("'").strip('"')  # remove quotes
-                    output_channel[match_emit.group(1)].append({output_val: {}})
-            outputs.append(output_channel)
-        log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
-        self.outputs = outputs
+        if self.component_type == "modules":
+            # get output values from main.nf after "output:". the names are always after "emit:"
+            if "output:" not in data:
+                log.debug(f"Could not find any outputs in {self.main_nf}")
+                return outputs
+            output_data = data.split("output:")[1].split("when:")[0]
+            regex_emit = r"emit:\s*([^)\s,]+)"
+            regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+            for line in output_data.split("\n"):
+                match_emit = re.search(regex_emit, line)
+                matches_elements = re.finditer(regex_elements, line)
+                if not match_emit:
+                    continue
+                output_channel = {match_emit.group(1): []}
+                for _, match_element in enumerate(matches_elements, start=1):
+                    output_val = None
+                    if match_element.group(3):
+                        output_val = match_element.group(3)
+                    elif match_element.group(4):
+                        output_val = match_element.group(4)
+                    if output_val:
+                        output_val = output_val.strip("'").strip('"')  # remove quotes
+                        output_channel[match_emit.group(1)].append({output_val: {}})
+                outputs.append(output_channel)
+            log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
+            self.outputs = outputs
+        elif self.component_type == "subworkflows":
+            # get output values from main.nf after "emit:". Can be named outputs or not.
+            if "emit:" not in data:
+                log.debug(f"Could not find any outputs in {self.main_nf}")
+                return outputs
+            output_data = data.split("emit:")[1].split("}")[0]
+            for line in output_data.split("\n"):
+                try:
+                    outputs.append(line.split("=")[0].split()[0])
+                except IndexError:
+                    # Empty lines
+                    pass
+            log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
+            self.outputs = outputs
diff --git a/nf_core/module-template/meta.yml b/nf_core/module-template/meta.yml
index c7c16dcb38..d9d1cc8ae8 100644
--- a/nf_core/module-template/meta.yml
+++ b/nf_core/module-template/meta.yml
@@ -53,11 +53,6 @@ input:
 ## TODO nf-core: Add a description of all of the variables used as output
 {% endif -%}
 output:
-  - versions:
-    - "versions.yml":
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
   - {{ 'bam:' if not_empty_template else "output:" }}
   #{% if has_meta -%} Only when we have meta
     - meta:
@@ -81,6 +76,11 @@ output:
           {% else -%}
           - edam: ""
           {%- endif %}
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
 
 authors:
   - "{{ author }}"
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 4f7ffd0739..4ad728d10b 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -95,6 +95,23 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
 
     # Confirm that all input and output channels are correctly specified
     if valid_meta_yml:
+        # confirm that the name matches the process name in main.nf
+        if meta_yaml["name"].upper() == module.process_name:
+            module.passed.append(
+                (
+                    "meta_name",
+                    "Correct name specified in `meta.yml`.",
+                    module.meta_yml,
+                )
+            )
+        else:
+            module.failed.append(
+                (
+                    "meta_name",
+                    f"Conflicting `process` name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)",
+                    module.meta_yml,
+                )
+            )
         # Check that inputs are specified in meta.yml
         if len(module.inputs) > 0 and "input" not in meta_yaml:
             module.failed.append(
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
index 367202155a..9bc344e7d1 100644
--- a/nf_core/pipeline-template/modules.json
+++ b/nf_core/pipeline-template/modules.json
@@ -8,12 +8,12 @@
                     {%- if fastqc %}
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
index d79f1c862d..d8989f4812 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf
@@ -26,7 +26,10 @@ process FASTQC {
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
 
-    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory)
+    // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222
+    // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml
index ee5507e06b..4827da7af2 100644
--- a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml
+++ b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml
@@ -16,35 +16,44 @@ tools:
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
       documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
       licence: ["GPL-2.0-only"]
+      identifier: biotools:fastqc
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
   - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.html":
+          type: file
+          description: FastQC report
+          pattern: "*_{fastqc.html}"
   - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.zip":
+          type: file
+          description: FastQC report archive
+          pattern: "*_{fastqc.zip}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@drpatelh"
   - "@grst"
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 70edae4d99..e9d79a074e 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
@@ -23,17 +23,14 @@ 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[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("fastqc_versions_single") }
+                { 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[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() }
             )
         }
     }
@@ -54,16 +51,14 @@ nextflow_process {
 
         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("fastqc_versions_paired") }
+                { 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() }
             )
         }
     }
@@ -83,13 +78,11 @@ nextflow_process {
 
         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("fastqc_versions_interleaved") }
+                { 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() }
             )
         }
     }
@@ -109,13 +102,11 @@ nextflow_process {
 
         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("fastqc_versions_bam") }
+                { 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() }
             )
         }
     }
@@ -138,22 +129,20 @@ nextflow_process {
 
         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("fastqc_versions_multiple") }
+                { 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() }
             )
         }
     }
@@ -173,21 +162,18 @@ nextflow_process {
 
         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("fastqc_versions_custom_prefix") }
+                { 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() }
             )
         }
     }
 
     test("sarscov2 single-end [fastq] - stub") {
 
-        options "-stub"
-
+    options "-stub"
         when {
             process {
                 """
@@ -201,12 +187,123 @@ nextflow_process {
 
         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("fastqc_stub") }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 interleaved [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [bam] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 multiple [fastq] - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 custom_prefix - stub") {
+
+    options "-stub"
+        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 snapshot(process.out).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 86f7c31154..d5db3092fb 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
@@ -1,88 +1,392 @@
 {
-    "fastqc_versions_interleaved": {
+    "sarscov2 custom_prefix": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:07.293713"
+        "timestamp": "2024-07-22T11:02:16.374038"
     },
-    "fastqc_stub": {
+    "sarscov2 single-end [fastq] - stub": {
         "content": [
-            [
-                "test.html",
-                "test.zip",
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:24.993809"
+    },
+    "sarscov2 custom_prefix - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "mysample",
+                            "single_end": true
+                        },
+                        "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:31:01.425198"
+        "timestamp": "2024-07-22T11:03:10.93942"
     },
-    "fastqc_versions_multiple": {
+    "sarscov2 interleaved [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:55.797907"
+        "timestamp": "2024-07-22T11:01:42.355718"
     },
-    "fastqc_versions_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:40:26.795862"
+        "timestamp": "2024-07-22T11:01:53.276274"
     },
-    "fastqc_versions_single": {
+    "sarscov2 multiple [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:27.043675"
+        "timestamp": "2024-07-22T11:02:05.527626"
     },
-    "fastqc_versions_paired": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:31.188871"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:34.273566"
+    },
+    "sarscov2 multiple [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:39:47.584191"
+        "timestamp": "2024-07-22T11:03:02.304411"
     },
-    "fastqc_versions_custom_prefix": {
+    "sarscov2 single-end [fastq]": {
         "content": [
             [
                 "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:01:19.095607"
+    },
+    "sarscov2 interleaved [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:02:44.640184"
+    },
+    "sarscov2 paired-end [bam] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+                ],
+                "zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-01-31T17:41:14.576531"
+        "timestamp": "2024-07-22T11:02:53.550742"
     }
 }
\ 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 329ddb4870..f1cd99b079 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
@@ -1,6 +1,5 @@
-name: multiqc
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.21
+  - bioconda::multiqc=1.24.1
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 47ac352f94..b9ccebdbbc 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
@@ -3,14 +3,16 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.21--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.25--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
     path(multiqc_config)
     path(extra_multiqc_config)
     path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -23,16 +25,22 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : ''
     def config = multiqc_config ? "--config $multiqc_config" : ''
     def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
     """
     multiqc \\
         --force \\
         $args \\
         $config \\
+        $prefix \\
         $extra_config \\
         $logo \\
+        $replace \\
+        $samples \\
         .
 
     cat <<-END_VERSIONS > versions.yml
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 45a9bc35e1..b16c187923 100644
--- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
+++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
@@ -1,5 +1,6 @@
 name: multiqc
-description: Aggregate results from bioinformatics analyses across many samples into a single report
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
 keywords:
   - QC
   - bioinformatics tools
@@ -12,40 +13,59 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
 input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
 output:
   - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
   - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
   - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@abhi18av"
   - "@bunop"
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 f1c4242ef2..33316a7ddb 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
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "multiqc"
 
+    config "./nextflow.config"
+
     test("sarscov2 single-end [fastqc]") {
 
         when {
@@ -17,6 +19,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -41,6 +45,8 @@ nextflow_process {
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -66,6 +72,8 @@ nextflow_process {
                 input[1] = []
                 input[2] = []
                 input[3] = []
+                input[4] = []
+                input[5] = []
                 """
             }
         }
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
index bfebd80298..b779e46924 100644
--- 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
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:48:55.657331"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:49.071937"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d"
+                "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-29T08:49:25.457567"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
-}
\ No newline at end of file
+}
diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
index 5b7e0ff143..f878bb31a2 100644
--- a/nf_core/pipeline-template/workflows/pipeline.nf
+++ b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -95,7 +95,9 @@ workflow {{ short_name|upper }} {
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        [],
+        []
     )
 {% endif %}
     emit:
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index b366ddfb51..cedae62f11 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -11,11 +11,12 @@
 
 import questionary
 import rich
+import ruamel.yaml
 
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
-from nf_core.pipelines.lint_utils import console
+from nf_core.pipelines.lint_utils import console, run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -45,6 +46,7 @@ def __init__(
         self,
         directory,
         fail_warned=False,
+        fix=False,
         remote_url=None,
         branch=None,
         no_pull=False,
@@ -55,6 +57,7 @@ def __init__(
             component_type="subworkflows",
             directory=directory,
             fail_warned=fail_warned,
+            fix=fix,
             remote_url=remote_url,
             branch=branch,
             no_pull=no_pull,
@@ -214,6 +217,10 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False):
 
         # Otherwise run all the lint tests
         else:
+            # Update meta.yml file if requested
+            if self.fix:
+                self.update_meta_yml_file(swf)
+
             if self.repo_type == "pipeline" and self.modules_json:
                 # Set correct sha
                 version = self.modules_json.get_subworkflow_version(swf.component_name, swf.repo_url, swf.org)
@@ -230,3 +237,56 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False):
                 self.failed += warned
 
             self.failed += [LintResult(swf, *s) for s in swf.failed]
+
+    def update_meta_yml_file(self, swf):
+        """
+        Update the meta.yml file with the correct inputs and outputs
+        """
+        yaml = ruamel.yaml.YAML()
+        yaml.preserve_quotes = True
+        yaml.indent(mapping=2, sequence=2, offset=0)
+
+        # Read meta.yml
+        with open(swf.meta_yml) as fh:
+            meta_yaml = yaml.load(fh)
+        meta_yaml_corrected = meta_yaml.copy()
+        # Obtain inputs and outputs from main.nf
+        swf.get_inputs_from_main_nf()
+        swf.get_outputs_from_main_nf()
+
+        # Compare inputs and add them if missing
+        if "input" in meta_yaml:
+            # Delete inputs from meta.yml which are not present in main.nf
+            meta_yaml_corrected["input"] = [
+                input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs
+            ]
+            # Obtain inputs from main.nf missing in meta.yml
+            inputs_correct = [
+                list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs
+            ]
+            inputs_missing = [input for input in swf.inputs if input not in inputs_correct]
+            # Add missing inputs to meta.yml
+            for missing_input in inputs_missing:
+                meta_yaml_corrected["input"].append({missing_input: {"description": ""}})
+
+        if "output" in meta_yaml:
+            # Delete outputs from meta.yml which are not present in main.nf
+            meta_yaml_corrected["output"] = [
+                output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs
+            ]
+            # Obtain output from main.nf missing in meta.yml
+            outputs_correct = [
+                list(output.keys())[0]
+                for output in meta_yaml_corrected["output"]
+                if list(output.keys())[0] in swf.outputs
+            ]
+            outputs_missing = [output for output in swf.outputs if output not in outputs_correct]
+            # Add missing inputs to meta.yml
+            for missing_output in outputs_missing:
+                meta_yaml_corrected["output"].append({missing_output: {"description": ""}})
+
+        # Write corrected meta.yml to file
+        with open(swf.meta_yml, "w") as fh:
+            log.info(f"Updating {swf.meta_yml}")
+            yaml.dump(meta_yaml_corrected, fh)
+            run_prettier_on_file(fh.name)
diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py
index 24e75eddbf..be282bc453 100644
--- a/nf_core/subworkflows/lint/meta_yml.py
+++ b/nf_core/subworkflows/lint/meta_yml.py
@@ -1,4 +1,5 @@
 import json
+import logging
 from pathlib import Path
 
 import jsonschema.validators
@@ -6,6 +7,8 @@
 
 import nf_core.components.components_utils
 
+log = logging.getLogger(__name__)
+
 
 def meta_yml(subworkflow_lint_object, subworkflow):
     """
@@ -65,6 +68,8 @@ def meta_yml(subworkflow_lint_object, subworkflow):
                     subworkflow.passed.append(("meta_input", f"`{input}` specified", subworkflow.meta_yml))
                 else:
                     subworkflow.failed.append(("meta_input", f"`{input}` missing in `meta.yml`", subworkflow.meta_yml))
+        else:
+            log.debug(f"No inputs specified in subworkflow `main.nf`: {subworkflow.component_name}")
 
         if "output" in meta_yaml:
             meta_output = [list(x.keys())[0] for x in meta_yaml["output"]]
@@ -75,6 +80,8 @@ def meta_yml(subworkflow_lint_object, subworkflow):
                     subworkflow.failed.append(
                         ("meta_output", f"`{output}` missing in `meta.yml`", subworkflow.meta_yml)
                     )
+        else:
+            log.debug(f"No outputs specified in subworkflow `main.nf`: {subworkflow.component_name}")
 
         # confirm that the name matches the process name in main.nf
         if meta_yaml["name"].upper() == subworkflow.workflow_name:
diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py
index f4adedfcb5..5372807987 100644
--- a/tests/modules/test_lint.py
+++ b/tests/modules/test_lint.py
@@ -210,14 +210,6 @@ def test_modules_lint_new_modules(self):
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
-    def test_modules_lint_update_meta_yml(self):
-        """update the meta.yml of a module"""
-        module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules, fix=True)
-        module_lint.lint(print_results=False, module="fastqc")
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.passed) > 0
-        assert len(module_lint.warned) >= 0
-
     def test_modules_lint_no_gitlab(self):
         """Test linting a pipeline with no modules installed"""
         self.mods_remove.remove("fastqc", force=True)
@@ -282,7 +274,7 @@ def test_modules_lint_patched_modules(self):
                 all_modules=True,
             )
 
-        assert len(module_lint.failed) == 1
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 
@@ -313,6 +305,14 @@ def test_modules_lint_check_url(self):
                 len(mocked_ModuleLint.failed) == failed
             ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}."
 
+    def test_modules_lint_update_meta_yml(self):
+        """update the meta.yml of a module"""
+        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules, fix=True)
+        module_lint.lint(print_results=False, module="bpipe/test")
+        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.passed) > 0
+        assert len(module_lint.warned) >= 0
+
     def test_modules_lint_snapshot_file(self):
         """Test linting a module with a snapshot file"""
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
@@ -521,25 +521,6 @@ def test_modules_meta_yml_incorrect_licence_field(self):
         assert len(module_lint.warned) >= 0
         assert module_lint.failed[0].lint_test == "meta_yml_valid"
 
-    def test_modules_meta_yml_input_mismatch(self):
-        """Test linting a module with an extra entry in input fields in meta.yml compared to module.input"""
-        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
-            main_nf = fh.read()
-        main_nf_new = main_nf.replace("path bam", "path bai")
-        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-            fh.write(main_nf_new)
-        module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
-        module_lint.lint(print_results=False, module="bpipe/test")
-        with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
-            fh.write(main_nf)
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert len(module_lint.passed) >= 0
-        assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}"
-        lint_tests = [x.lint_test for x in module_lint.warned]
-        # check that it is there twice:
-        assert lint_tests.count("meta_input_meta_only") == 1
-        assert lint_tests.count("meta_input_main_only") == 1
-
     def test_modules_meta_yml_output_mismatch(self):
         """Test linting a module with an extra entry in output fields in meta.yml compared to module.output"""
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh:
@@ -551,13 +532,9 @@ def test_modules_meta_yml_output_mismatch(self):
         module_lint.lint(print_results=False, module="bpipe/test")
         with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh:
             fh.write(main_nf)
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0
-        assert len(module_lint.warned) == 2
-        lint_tests = [x.lint_test for x in module_lint.warned]
-        # check that it is there twice:
-        assert lint_tests.count("meta_output_meta_only") == 1
-        assert lint_tests.count("meta_output_main_only") == 1
+        assert "Module `meta.yml` does not match `main.nf`" in module_lint.failed[0].message
 
     def test_modules_meta_yml_incorrect_name(self):
         """Test linting a module with an incorrect name in meta.yml"""
diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py
index c3eb94d374..2f60cd4a20 100644
--- a/tests/modules/test_patch.py
+++ b/tests/modules/test_patch.py
@@ -21,10 +21,10 @@
 testing if the update commands works correctly with patch files
 """
 
-ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2"
-CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f"
-SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e"
-FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73"
+ORG_SHA = "3dc7c14d29af40f1a0871a675364e437559d97a8"
+CORRECT_SHA = "63e780200600e340365b669f9c673b670764c569"
+SUCCEED_SHA = "0d0515c3f11266e1314e129bec3e308f804c8dc7"
+FAIL_SHA = "cb64a5c1ef85619b89ab99dec2e9097fe84e1dc8"
 BISMARK_ALIGN = "bismark/align"
 REPO_NAME = "nf-core-test"
 PATCH_BRANCH = "patch-tester"
@@ -76,7 +76,7 @@ def test_create_patch_no_change(self):
         module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
 
         # Check that no patch file has been added to the directory
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml"}
 
         # Check the 'modules.json' contains no patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -94,7 +94,7 @@ def test_create_patch_change(self):
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -127,7 +127,7 @@ def test_create_patch_try_apply_successful(self):
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -153,7 +153,7 @@ def test_create_patch_try_apply_successful(self):
         update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA)
 
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -195,7 +195,7 @@ def test_create_patch_try_apply_failed(self):
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -234,7 +234,7 @@ def test_create_patch_update_success(self):
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -254,7 +254,7 @@ def test_create_patch_update_success(self):
         assert update_obj.update(BISMARK_ALIGN)
 
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -295,7 +295,7 @@ def test_create_patch_update_fail(self):
 
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
         # Check that a patch file with the correct name has been created
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -349,7 +349,7 @@ def test_remove_patch(self):
 
         # Check that a patch file with the correct name has been created
         patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff"
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn}
 
         # Check the 'modules.json' contains a patch file for the module
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
@@ -361,7 +361,7 @@ def test_remove_patch(self):
             mock_questionary.unsafe_ask.return_value = True
             patch_obj.remove(BISMARK_ALIGN)
         # Check that the diff file has been removed
-        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"}
+        assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml"}
 
         # Check that the 'modules.json' entry has been removed
         modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir)
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 56574b865c..d94b55b3d3 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -63,6 +63,14 @@ def test_subworkflows_lint_multiple_remotes(self):
         assert len(subworkflow_lint.passed) > 0
         assert len(subworkflow_lint.warned) >= 0
 
+    def test_subworkflows_lint_update_meta_yml(self):
+        """update the meta.yml of a subworkflow"""
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules, fix=True)
+        subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+        assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        assert len(subworkflow_lint.passed) > 0
+        assert len(subworkflow_lint.warned) >= 0
+
     def test_subworkflows_lint_snapshot_file(self):
         """Test linting a subworkflow with a snapshot file"""
         subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules)
diff --git a/tests/test_modules.py b/tests/test_modules.py
index 0e16497176..d0692236e8 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -7,7 +7,7 @@
 import pytest
 import requests_cache
 import responses
-import yaml
+import ruamel.yaml
 
 import nf_core.modules
 import nf_core.modules.create
@@ -16,6 +16,7 @@
 import nf_core.modules.remove
 import nf_core.pipelines.create.create
 from nf_core import __version__
+from nf_core.pipelines.lint_utils import run_prettier_on_file
 from nf_core.utils import NFCoreYamlConfig
 
 from .utils import (
@@ -28,11 +29,15 @@
     create_tmp_pipeline,
     mock_anaconda_api_calls,
     mock_biocontainers_api_calls,
+    mock_biotools_api_calls,
 )
 
 
 def create_modules_repo_dummy(tmp_dir):
     """Create a dummy copy of the nf-core/modules repo"""
+    yaml = ruamel.yaml.YAML()
+    yaml.preserve_quotes = True
+    yaml.indent(mapping=2, sequence=2, offset=0)
 
     root_dir = Path(tmp_dir, "modules")
     Path(root_dir, "modules", "nf-core").mkdir(parents=True)
@@ -42,13 +47,14 @@ def create_modules_repo_dummy(tmp_dir):
     nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core")
     with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
         yaml.dump(nf_core_yml.model_dump(), fh)
-    # mock biocontainers and anaconda response
+    # mock biocontainers and anaconda response and biotools response
     with responses.RequestsMock() as rsps:
         mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
         mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0")
+        mock_biotools_api_calls(rsps, "bpipe")
         # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules
         module_create = nf_core.modules.create.ModuleCreate(
-            root_dir, "bpipe/test", "@author", "process_single", False, False
+            root_dir, "bpipe/test", "@author", "process_single", True, False
         )
         with requests_cache.disabled():
             assert module_create.create()
@@ -57,10 +63,11 @@ def create_modules_repo_dummy(tmp_dir):
     meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml")
 
     with open(str(meta_yml_path)) as fh:
-        meta_yml = yaml.safe_load(fh)
+        meta_yml = yaml.load(fh)
     del meta_yml["tools"][0]["bpipe"]["doi"]
     with open(str(meta_yml_path), "w") as fh:
         yaml.dump(meta_yml, fh)
+        run_prettier_on_file(fh.name)
     # Add dummy content to main.nf.test.snap
     test_snap_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap")
 
diff --git a/tests/utils.py b/tests/utils.py
index 1d5a8a115d..6f4b73cccc 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -98,6 +98,15 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers
     rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200)
 
 
+def mock_biotools_api_calls(rsps: responses.RequestsMock, module: str) -> None:
+    """Mock biotools api calls for module"""
+    biotools_api_url = f"https://bio.tools/api/t/?q={module}&format=json"
+    biotools_mock = {
+        "list": [{"name": "Bpipe", "biotoolsCURIE": "biotools:bpipe"}],
+    }
+    rsps.get(biotools_api_url, json=biotools_mock, status=200)
+
+
 def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]:
     """Create a new Pipeline for testing"""