diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 0efea13ec9..053a146bdf 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -54,7 +54,12 @@
 )
 from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE
 from nf_core.pipelines.download import DownloadError
-from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
+from nf_core.utils import (
+    check_if_outdated,
+    nfcore_logo,
+    rich_force_colors,
+    setup_nfcore_dir,
+)
 
 # Set up logging as the root logger
 # Submodules should all traverse back to this
@@ -85,7 +90,14 @@
         },
         {
             "name": "For developers",
-            "commands": ["create", "lint", "bump-version", "sync", "schema", "create-logo"],
+            "commands": [
+                "create",
+                "lint",
+                "bump-version",
+                "sync",
+                "schema",
+                "create-logo",
+            ],
         },
     ],
     "nf-core modules": [
@@ -257,7 +269,13 @@ def pipelines(ctx):
 @click.option("-d", "--description", type=str, help="A short description of your pipeline")
 @click.option("-a", "--author", type=str, help="Name of the main author(s)")
 @click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use")
-@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
+@click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Overwrite output directory if it already exists",
+)
 @click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
 @click.option(
@@ -270,7 +288,17 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
     """
     Create a new pipeline using the nf-core template.
     """
-    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
+    pipelines_create(
+        ctx,
+        name,
+        description,
+        author,
+        version,
+        force,
+        outdir,
+        template_yaml,
+        organisation,
+    )
 
 
 # nf-core pipelines lint
@@ -346,7 +374,19 @@ def command_pipelines_lint(
     """
     Check pipeline code against nf-core guidelines.
     """
-    pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
+    pipelines_lint(
+        ctx,
+        directory,
+        release,
+        fix,
+        key,
+        show_passed,
+        fail_ignored,
+        fail_warned,
+        markdown,
+        json,
+        sort_by,
+    )
 
 
 # nf-core pipelines download
@@ -556,7 +596,18 @@ def command_pipelines_launch(
     """
     Launch a pipeline using a web GUI or command line prompts.
     """
-    pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url)
+    pipelines_launch(
+        ctx,
+        pipeline,
+        id,
+        revision,
+        command_only,
+        params_in,
+        params_out,
+        save_all,
+        show_hidden,
+        url,
+    )
 
 
 # nf-core pipelines list
@@ -613,12 +664,28 @@ def command_pipelines_list(ctx, keywords, sort, json, show_archived):
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
 def command_pipelines_sync(
-    ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr
+    ctx,
+    directory,
+    from_branch,
+    pull_request,
+    github_repository,
+    username,
+    template_yaml,
+    force_pr,
 ):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
     """
-    pipelines_sync(ctx, directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+    pipelines_sync(
+        ctx,
+        directory,
+        from_branch,
+        pull_request,
+        github_repository,
+        username,
+        template_yaml,
+        force_pr,
+    )
 
 
 # nf-core pipelines bump-version
@@ -650,7 +717,14 @@ def command_pipelines_bump_version(ctx, new_version, directory, nextflow):
 # nf-core pipelines create-logo
 @pipelines.command("create-logo")
 @click.argument("logo-text", metavar="<logo_text>")
-@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(),
+    default=".",
+    help="Directory to save the logo in.",
+)
 @click.option(
     "-n",
     "--name",
@@ -885,7 +959,13 @@ def command_modules_list_local(ctx, keywords, json, directory):  # pylint: disab
 # nf-core modules install
 @modules.command("install")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -919,7 +999,13 @@ def command_modules_install(ctx, tool, directory, prompt, force, sha):
 # nf-core modules update
 @modules.command("update")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -990,13 +1076,31 @@ def command_modules_update(
     """
     Update DSL2 modules within a pipeline.
     """
-    modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output)
+    modules_update(
+        ctx,
+        tool,
+        directory,
+        force,
+        prompt,
+        sha,
+        install_all,
+        preview,
+        save_diff,
+        update_deps,
+        limit_output,
+    )
 
 
 # nf-core modules patch
 @modules.command("patch")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1016,7 +1120,13 @@ def command_modules_patch(ctx, tool, directory, remove):
 # nf-core modules remove
 @modules.command("remove")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1036,7 +1146,14 @@ def command_modules_remove(ctx, directory, tool):
 @modules.command("create")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
-@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    metavar="<directory>",
+)
 @click.option(
     "-a",
     "--author",
@@ -1099,6 +1216,12 @@ def command_modules_remove(ctx, directory, tool):
     default=False,
     help="Migrate a module with pytest tests to nf-test",
 )
+@click.option(
+    "--migrate-pytest-hard",
+    is_flag=True,
+    default=False,
+    help="Try hard when migrating pytest tests",
+)
 def command_modules_create(
     ctx,
     tool,
@@ -1112,6 +1235,7 @@ def command_modules_create(
     conda_package_version,
     empty_template,
     migrate_pytest,
+    migrate_pytest_hard,
 ):
     """
     Create a new DSL2 module from the nf-core template.
@@ -1129,13 +1253,20 @@ def command_modules_create(
         conda_package_version,
         empty_template,
         migrate_pytest,
+        migrate_pytest_hard,
     )
 
 
 # nf-core modules test
 @modules.command("test")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-v",
     "--verbose",
@@ -1178,19 +1309,52 @@ def command_modules_create(
     default=False,
     help="Migrate a module with pytest tests to nf-test",
 )
-def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest, verbose):
+@click.option(
+    "--migrate-pytest-hard",
+    is_flag=True,
+    default=False,
+    help="Try hard when migrating pytest tests",
+)
+def command_modules_test(
+    ctx,
+    tool,
+    directory,
+    no_prompts,
+    update,
+    once,
+    profile,
+    migrate_pytest,
+    migrate_pytest_hard,
+    verbose,
+):
     """
     Run nf-test for a module.
     """
     if verbose:
         ctx.obj["verbose"] = verbose
-    modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest)
+    modules_test(
+        ctx,
+        tool,
+        directory,
+        no_prompts,
+        update,
+        once,
+        profile,
+        migrate_pytest,
+        migrate_pytest_hard,
+    )
 
 
 # nf-core modules lint
 @modules.command("lint")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1231,17 +1395,47 @@ def command_modules_test(ctx, tool, directory, no_prompts, update, once, profile
     is_flag=True,
     help="Fix the module version if a newer version is available",
 )
-def command_modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
+def command_modules_lint(
+    ctx,
+    tool,
+    directory,
+    registry,
+    key,
+    all,
+    fail_warned,
+    local,
+    passed,
+    sort_by,
+    fix_version,
+):
     """
     Lint one or more modules in a directory.
     """
-    modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version)
+    modules_lint(
+        ctx,
+        tool,
+        directory,
+        registry,
+        key,
+        all,
+        fail_warned,
+        local,
+        passed,
+        sort_by,
+        fix_version,
+    )
 
 
 # nf-core modules info
 @modules.command("info")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1260,7 +1454,13 @@ def command_modules_info(ctx, tool, directory):
 # nf-core modules bump-versions
 @modules.command("bump-versions")
 @click.pass_context
-@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument(
+    "tool",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="<tool> or <tool/subtool>",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1321,7 +1521,14 @@ def subworkflows(ctx, git_remote, branch, no_pull):
 @subworkflows.command("create")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
-@click.option("-d", "--dir", "directory", type=click.Path(exists=True), default=".", metavar="<directory>")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    metavar="<directory>",
+)
 @click.option(
     "-a",
     "--author",
@@ -1352,7 +1559,13 @@ def command_subworkflows_create(ctx, subworkflow, directory, author, force, migr
 # nf-core subworkflows test
 @subworkflows.command("test")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1440,7 +1653,13 @@ def command_subworkflows_list_local(ctx, keywords, json, directory):  # pylint:
 # nf-core subworkflows lint
 @subworkflows.command("lint")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1480,13 +1699,30 @@ def command_subworkflows_lint(ctx, subworkflow, directory, registry, key, all, f
     """
     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,
+    )
 
 
 # nf-core subworkflows info
 @subworkflows.command("info")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1505,7 +1741,13 @@ def command_subworkflows_info(ctx, subworkflow, directory):
 # nf-core subworkflows install
 @subworkflows.command("install")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1545,7 +1787,13 @@ def command_subworkflows_install(ctx, subworkflow, directory, prompt, force, sha
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1564,7 +1812,13 @@ def command_subworkflows_remove(ctx, directory, subworkflow):
 # nf-core subworkflows update
 @subworkflows.command("update")
 @click.pass_context
-@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
+@click.argument(
+    "subworkflow",
+    type=str,
+    callback=normalize_case,
+    required=False,
+    metavar="subworkflow name",
+)
 @click.option(
     "-d",
     "--dir",
@@ -1643,7 +1897,17 @@ def command_subworkflows_update(
     Update DSL2 subworkflow within a pipeline.
     """
     subworkflows_update(
-        ctx, subworkflow, directory, force, prompt, sha, install_all, preview, save_diff, update_deps, limit_output
+        ctx,
+        subworkflow,
+        directory,
+        force,
+        prompt,
+        sha,
+        install_all,
+        preview,
+        save_diff,
+        update_deps,
+        limit_output,
     )
 
 
@@ -1772,7 +2036,14 @@ def command_schema_docs(schema_path, output, format, force, columns):
 # nf-core create-logo (deprecated)
 @nf_core_cli.command("create-logo", deprecated=True, hidden=True)
 @click.argument("logo-text", metavar="<logo_text>")
-@click.option("-d", "--dir", "directory", type=click.Path(), default=".", help="Directory to save the logo in.")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(),
+    default=".",
+    help="Directory to save the logo in.",
+)
 @click.option(
     "-n",
     "--name",
@@ -1849,14 +2120,30 @@ def command_create_logo(logo_text, directory, name, theme, width, format, force)
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def command_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
+def command_sync(
+    directory,
+    from_branch,
+    pull_request,
+    github_repository,
+    username,
+    template_yaml,
+    force_pr,
+):
     """
     Use `nf-core pipelines sync` instead.
     """
     log.warning(
         "The `[magenta]nf-core sync[/]` command is deprecated. Use `[magenta]nf-core pipelines sync[/]` instead."
     )
-    pipelines_sync(directory, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
+    pipelines_sync(
+        directory,
+        from_branch,
+        pull_request,
+        github_repository,
+        username,
+        template_yaml,
+        force_pr,
+    )
 
 
 # nf-core bump-version (deprecated)
@@ -1976,7 +2263,18 @@ def command_launch(
     log.warning(
         "The `[magenta]nf-core launch[/]` command is deprecated. Use `[magenta]nf-core pipelines launch[/]` instead."
     )
-    pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, save_all, show_hidden, url)
+    pipelines_launch(
+        ctx,
+        pipeline,
+        id,
+        revision,
+        command_only,
+        params_in,
+        params_out,
+        save_all,
+        show_hidden,
+        url,
+    )
 
 
 # nf-core create-params-file (deprecated)
@@ -2202,7 +2500,19 @@ def command_lint(
     log.warning(
         "The `[magenta]nf-core lint[/]` command is deprecated. Use `[magenta]nf-core pipelines lint[/]` instead."
     )
-    pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_warned, markdown, json, sort_by)
+    pipelines_lint(
+        ctx,
+        directory,
+        release,
+        fix,
+        key,
+        show_passed,
+        fail_ignored,
+        fail_warned,
+        markdown,
+        json,
+        sort_by,
+    )
 
 
 # nf-core create (deprecated)
@@ -2216,7 +2526,13 @@ def command_lint(
 @click.option("-d", "--description", type=str, help="A short description of your pipeline")
 @click.option("-a", "--author", type=str, help="Name of the main author(s)")
 @click.option("--version", type=str, default="1.0.0dev", help="The initial version number to use")
-@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite output directory if it already exists")
+@click.option(
+    "-f",
+    "--force",
+    is_flag=True,
+    default=False,
+    help="Overwrite output directory if it already exists",
+)
 @click.option("-o", "--outdir", help="Output directory for new pipeline (default: pipeline name)")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
 @click.option("--plain", is_flag=True, help="Use the standard nf-core template")
@@ -2227,14 +2543,35 @@ def command_lint(
     help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
 )
 @click.pass_context
-def command_create(ctx, name, description, author, version, force, outdir, template_yaml, plain, organisation):
+def command_create(
+    ctx,
+    name,
+    description,
+    author,
+    version,
+    force,
+    outdir,
+    template_yaml,
+    plain,
+    organisation,
+):
     """
     Use `nf-core pipelines create` instead.
     """
     log.warning(
         "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
     )
-    pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
+    pipelines_create(
+        ctx,
+        name,
+        description,
+        author,
+        version,
+        force,
+        outdir,
+        template_yaml,
+        organisation,
+    )
 
 
 # Main script is being run - launch the CLI
diff --git a/nf_core/commands_modules.py b/nf_core/commands_modules.py
index 57c8e9777c..30e8137cfe 100644
--- a/nf_core/commands_modules.py
+++ b/nf_core/commands_modules.py
@@ -175,6 +175,7 @@ def modules_create(
     conda_package_version,
     empty_template,
     migrate_pytest,
+    migrate_pytest_hard,
 ):
     """
     Create a new DSL2 module from the nf-core template.
@@ -194,6 +195,10 @@ def modules_create(
     elif no_meta:
         has_meta = False
 
+    if migrate_pytest_hard and not migrate_pytest:
+        log.error("--migrate_pytest_hard can only allowed in combination with --migrate_pytest.")
+        sys.exit(1)
+
     from nf_core.modules.create import ModuleCreate
 
     # Run function
@@ -209,6 +214,7 @@ def modules_create(
             conda_package_version,
             empty_template,
             migrate_pytest,
+            migrate_pytest_hard,
         )
         module_create.create()
     except UserWarning as e:
@@ -219,7 +225,17 @@ def modules_create(
         sys.exit(1)
 
 
-def modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrate_pytest):
+def modules_test(
+    ctx,
+    tool,
+    directory,
+    no_prompts,
+    update,
+    once,
+    profile,
+    migrate_pytest,
+    migrate_pytest_hard,
+):
     """
     Run nf-test for a module.
 
@@ -227,6 +243,10 @@ def modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrat
     """
     from nf_core.components.components_test import ComponentsTest
 
+    if migrate_pytest_hard and not migrate_pytest:
+        log.error("--migrate_pytest_hard can only allowed in combination with --migrate_pytest.")
+        sys.exit(1)
+
     if migrate_pytest:
         modules_create(
             ctx,
@@ -241,6 +261,7 @@ def modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrat
             conda_package_version=None,
             empty_template=False,
             migrate_pytest=migrate_pytest,
+            migrate_pytest_hard=migrate_pytest_hard,
         )
     try:
         module_tester = ComponentsTest(
@@ -261,7 +282,19 @@ def modules_test(ctx, tool, directory, no_prompts, update, once, profile, migrat
         sys.exit(1)
 
 
-def modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
+def modules_lint(
+    ctx,
+    tool,
+    directory,
+    registry,
+    key,
+    all,
+    fail_warned,
+    local,
+    passed,
+    sort_by,
+    fix_version,
+):
     """
     Lint one or more modules in a directory.
 
diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index c71b128415..7e33c93cc0 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -40,6 +40,7 @@ def __init__(
         conda_version: Optional[str] = None,
         empty_template: bool = False,
         migrate_pytest: bool = False,
+        migrate_pytest_hard=False,
     ):
         super().__init__(component_type, directory)
         self.directory = directory
@@ -61,6 +62,9 @@ def __init__(
         self.file_paths: Dict[str, Path] = {}
         self.not_empty_template = not empty_template
         self.migrate_pytest = migrate_pytest
+        self.migrate_pytest_hard = migrate_pytest_hard
+        self.pytest_units_str = None
+        self.pytest_has_nextflow_config = False
 
     def create(self) -> bool:
         """
@@ -137,6 +141,23 @@ def create(self) -> bool:
         # Check existence of directories early for fast-fail
         self.file_paths = self._get_component_dirs()
 
+        component_outputs = {}  # output: meta_data
+        if self.migrate_pytest and self.migrate_pytest_hard:
+            # Extract outputs data
+            main_nf_data = Path(
+                self.directory, self.component_type, self.org, self.component_dir, "main.nf"
+            ).read_text()
+            if "output:" not in main_nf_data:
+                log.debug(f"Could not find any outputs in {self.component_name}")
+            else:
+                component_outputs_data = main_nf_data.split("output:")[1].split("when:")[0]
+                matches = re.findall(r"(.*)emit:\s*([^)\s,]+)", component_outputs_data, re.MULTILINE)
+                for match in matches:
+                    component_outputs[match[1]] = match[0]
+                log.debug(
+                    f"Found {len(component_outputs)} outputs in {self.component_name}: {component_outputs.keys()}"
+                )
+
         if self.migrate_pytest:
             # Rename the component directory to old
             component_old_dir = Path(str(self.component_dir) + "_old")
@@ -160,12 +181,22 @@ def create(self) -> bool:
         not_alphabet = re.compile(r"[^a-zA-Z]")
         self.org_alphabet = not_alphabet.sub("", self.org)
 
+        # Extract pytest nextflow config
+        pytest_nextflow_config_contents = None
+        if self.migrate_pytest:
+            pytest_nextflow_config_contents = self._extract_nextflow_config()
+
+        # Extract pytest units
+        if self.migrate_pytest and self.migrate_pytest_hard:
+            self._extract_pytest_units(component_outputs)
+
         # Create component template with jinja2
         assert self._render_template()
         log.info(f"Created component template: '{self.component_name}'")
 
         if self.migrate_pytest:
             self._copy_old_files(component_old_path)
+            self._copy_nextflow_config(pytest_nextflow_config_contents)
             log.info("Migrate pytest tests: Copied original module files to new module")
             shutil.rmtree(component_old_path)
             self._print_and_delete_pytest_files()
@@ -458,6 +489,8 @@ def _copy_old_files(self, component_old_path):
                     component_old_path / "templates",
                     self.file_paths["environment.yml"].parent / "templates",
                 )
+
+    def _extract_nextflow_config(self):
         # Create a nextflow.config file if it contains information other than publishDir
         pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
         nextflow_config = pytest_dir / "nextflow.config"
@@ -468,20 +501,29 @@ def _copy_old_files(self, component_old_path):
                     if "publishDir" not in line and line.strip() != "":
                         config_lines += line
             # if the nextflow.config file only contained publishDir, non_publish_dir_lines will be 11 characters long (`process {\n}`)
-            if len(config_lines) > 11:
-                log.debug("Copying nextflow.config file from pytest tests")
-                with open(
-                    Path(
-                        self.directory,
-                        self.component_type,
-                        self.org,
-                        self.component_dir,
-                        "tests",
-                        "nextflow.config",
-                    ),
-                    "w+",
-                ) as ofh:
-                    ofh.write(config_lines)
+            if not re.match(r"^\s*process\s*{\s*}\s*$", config_lines, re.DOTALL):
+                self.pytest_has_nextflow_config = True
+                return config_lines
+
+        return None
+
+    def _copy_nextflow_config(self, config_lines):
+        if config_lines is None:
+            return
+
+        log.debug("Copying nextflow.config file from pytest tests")
+        with open(
+            Path(
+                self.directory,
+                self.component_type,
+                self.org,
+                self.component_dir,
+                "tests",
+                "nextflow.config",
+            ),
+            "w+",
+        ) as ofh:
+            ofh.write(config_lines)
 
     def _print_and_delete_pytest_files(self):
         """Prompt if pytest files should be deleted and printed to stdout"""
@@ -519,3 +561,261 @@ def _print_and_delete_pytest_files(self):
         with open(modules_yml, "w") as fh:
             yaml.dump(yml_file, fh)
         run_prettier_on_file(modules_yml)
+
+    def _extract_pytest_units(self, component_outputs):
+        pytest_dir = Path(self.directory, "tests", self.component_type, self.org, self.component_dir)
+        main_nf_contents = Path(pytest_dir, "main.nf").read_text(encoding="UTF-8")
+
+        include_statements = re.findall(r"include\s*{\s*(\w+)([\sas]+)?(\w+)?\s*}", main_nf_contents)
+
+        log.debug(f"Found {len(include_statements)} include statements {include_statements}")
+
+        if len(include_statements) > 1:
+            raise ValueError("Multiple include statements are not yet supported")
+
+        main_nf_workflows = re.findall(r"workflow\s*(\w+)\s*{([^}]+)}", main_nf_contents, re.DOTALL)
+
+        log.debug(f"Found {len(main_nf_workflows)} workflows {[x[0] for x in main_nf_workflows]}")
+
+        nf_test_workflow = []
+        for workflow in main_nf_workflows:
+            workflow_name = workflow[0]
+            workflow_content = str(workflow[1])
+
+            log.debug(f"Looking for NXF symbols in workflow {workflow_name}")
+
+            nxf_symbols = self._extract_pytest_nxf_symbols(workflow_content)
+
+            invoked_components = re.findall(r"(\w+)\s*\(([^\)]*)\)", workflow_content, re.DOTALL)
+
+            invoked_components = [c for c in invoked_components if c[0] != "file"]
+
+            log.debug(
+                f"Found {len(invoked_components)} component(s) invoked by '{workflow_name}': {invoked_components}"
+            )
+
+            if len(invoked_components) > 1:
+                raise ValueError(
+                    f"Test workflow {workflow_name} invokes multiple components. This is not supported currently."
+                )
+
+            # TODO: Generalize to multiple components
+            invoked_component = invoked_components[0]
+
+            # invoked_component_name = invoked_component[0].strip()
+            invoked_component_args = invoked_component[1].strip()
+
+            extracted_component_args = self._extract_pytest_component_args(invoked_component_args, nxf_symbols)
+
+            nf_test_workflow.append({"name": workflow_name.replace("_", "-"), "input": extracted_component_args})
+
+        test_units_str = ""
+        for test in nf_test_workflow:
+            test_name = test["name"]
+            log.debug(f"Scaffolding nf-test '{test_name}'")
+
+            input_data_lines = self._make_nf_test_input(test["input"])
+            add_stub_option = "options '-stub'" if "stub" in test_name else ""
+
+            power_assertions = self._get_power_assertions(component_outputs, is_stub=("stub" in test_name))
+
+            test_unit_str = f"""
+    test("{test_name}") {{
+        {add_stub_option}
+        when {{
+            process {{
+                \"\"\"
+                {input_data_lines}
+                \"\"\"
+            }}
+        }}
+
+        then {{
+            assertAll(
+                {{ assert process.success }},
+                {power_assertions}
+            )
+        }}
+    }}
+    """
+            test_units_str += test_unit_str
+
+        self.pytest_units_str = test_units_str
+
+    def _extract_pytest_nxf_symbols(self, workflow_content: str) -> dict[str, str]:
+        symbols = {}
+        found_all = False
+
+        remaining_content = workflow_content
+        while not found_all:
+            match = self._extract_pytest_nxf_symbol_match(remaining_content)
+            if match:
+                match = match[0]
+
+                log.debug(f"Found symbol '{match[0]}' with data {match[1]}")
+                remaining_content = remaining_content.replace(f"{match[0]}={match[1]}", "", 1)
+                symbols[match[0].strip()] = match[1].strip()
+                continue
+
+            found_all = True
+
+        return symbols
+
+    def _extract_pytest_nxf_symbol_match(self, workflow_content):
+        # multiline list such as input = [etc]
+        list_match = re.findall(r"(\w+\s*)=(\s*\[.*?\n\s*\])", workflow_content, re.DOTALL)
+
+        if list_match != []:
+            return list_match
+
+        # second rule for multiline list such as input = [etc]
+        # The first rule might not be needed!
+        list_match = re.findall(r"(\w+\s*)=(\s*\[[^=]+\]\s+)", workflow_content, re.DOTALL)
+
+        if list_match != []:
+            return list_match
+
+        # simple list such as input = [ ]
+        list_match = re.findall(r"(\w+\s*)=(\s*\[\s*\])", workflow_content, re.DOTALL)
+
+        if list_match != []:
+            return list_match
+
+        # String match such as 'etc', "etc"
+        string_match = re.findall(r"(\w+\s*)=(\s*['\"][^'\"]*['\"])", workflow_content)
+
+        if string_match != []:
+            return string_match
+
+        # Number match such as 123.1
+        num_match = re.findall(r"(\w+\s*)=(\s*[\d\.]+)", workflow_content, re.DOTALL)
+
+        if num_match != []:
+            return num_match
+
+        # File match such as file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+        file_match = re.findall(r"(\w+\s*)=(\s*file\s*\(.*?\s*\))", workflow_content, re.DOTALL)
+
+        if file_match != []:
+            return file_match
+
+        return []
+
+    def _make_nf_test_input(self, input_data):
+        input_data_lines = ""
+        for index in range(len(input_data)):
+            arg_data = input_data[index]
+            if "\n" in arg_data:
+                input_data_str = self._indent_nf_test_arg(arg_data)
+            else:
+                input_data_str = arg_data.strip()
+
+            indent = ""
+            if index > 0:
+                indent = "\t\t\t\t"
+            input_data_lines += indent + f"input[{index}] = " + input_data_str + "\n"
+
+        return input_data_lines
+
+    def _indent_nf_test_arg(self, arg_data):
+        arg_data_lines = arg_data.split("\n")
+
+        return arg_data_lines[0].strip() + "\n" + "\n".join(["\t\t\t\t" + line.strip() for line in arg_data_lines[1:]])
+
+    def _extract_pytest_component_args(self, args_str: str, nxf_symbols: dict[str, str]) -> list[str]:
+        # No arg
+        if args_str == "":
+            return []
+
+        # Single argument
+        if args_str in nxf_symbols.keys():
+            return [nxf_symbols[args_str]]
+
+        # All arguments are named
+        match = re.match(r"^[\sa-zA-Z_,]+$", args_str, re.DOTALL)
+
+        if match:
+            # Double check that any arg name is not on the prohibited list
+            args_list = args_str.split(",")
+            prohibited_names = ["false", "true"]
+            has_prohibited = any([arg.strip() in prohibited_names for arg in args_list])
+            if not has_prohibited:
+                return [nxf_symbols[arg.strip()] for arg in args_str.split(",")]
+
+        # Split args while keeping brackets grouped
+        args = re.findall(r"\[.+\]|\w+|\[\]|[\w'\"]+", args_str)
+
+        if not args:
+            raise ValueError(f"Can not split args: {args_str}")
+
+        log.debug(f"Split args: {args_str} into: {args}")
+
+        # Replace the symbols embedded in list args
+        normalized_args = []
+        for arg in args:
+            if "[" in arg:
+                normalized_arg = self._replace_pytest_symbol_in_list_arg(arg, nxf_symbols)
+                normalized_args.append(normalized_arg)
+                continue
+
+            # For remaining args, try to replace symbol if possible
+            normalized_args.append(nxf_symbols[arg] if arg in nxf_symbols.keys() else arg)
+
+        return normalized_args
+
+    def _replace_pytest_symbol_in_list_arg(self, arg: str, nxf_symbols: dict[str, str]) -> str:
+        symbols = re.findall(r"[a-zA-Z_]+", arg)
+
+        for symbol in symbols:
+            arg = arg.replace(symbol, nxf_symbols[symbol] if symbol in nxf_symbols.keys() else symbol, 1)
+
+        return arg
+
+    def _get_power_assertions(self, component_outputs, is_stub):
+        power_assertions = "{ assert snapshot(process.out).match() }"
+
+        if is_stub:
+            return power_assertions
+
+        non_stable_outputs = ["bam", "txt", "log", "gz", "rds", "png"]
+
+        outputs_str = " ".join([f"{key} {value}" for (key, value) in component_outputs.items()]).lower()
+        has_non_stable = any([ns_output in outputs_str for ns_output in non_stable_outputs])
+
+        if not has_non_stable:
+            return power_assertions
+
+        power_assertions = "{ assert snapshot("
+        for output_name, output_meta in component_outputs.items():
+            if output_name == "versions":
+                continue
+
+            if "bam" in output_name or "bam" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tbam(process.out.{output_name}[0][1]).getReadsMD5(),"
+                continue
+
+            if "log" in output_name or "log" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tfile(process.out.{output_name}[0][1]).name,"
+                continue
+
+            if "gz" in output_name or "gz" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tpath(process.out.{output_name}[0][1]).linesGzip[3..7],"
+                continue
+
+            if "txt" in output_name or "txt" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tfile(process.out.{output_name}[0][1]).readLines()[3..7],"
+                continue
+
+            if "rds" in output_name or "rds" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tfile(process.out.{output_name}[0][1]).name,"
+                continue
+
+            if "png" in output_name or "png" in output_meta:
+                power_assertions += f"\n\t\t\t\t\tfile(process.out.{output_name}[0][1]).name,"
+                continue
+
+            power_assertions += f"\n\t\t\t\t\tprocess.out.{output_name},"
+
+        power_assertions += "\n\t\t\t\t\tprocess.out.versions\n\t\t\t\t\t).match()\n\t\t\t\t}"
+
+        return power_assertions
diff --git a/nf_core/module-template/tests/main.nf.test.j2 b/nf_core/module-template/tests/main.nf.test.j2
index a50ecc6a07..c29585b52b 100644
--- a/nf_core/module-template/tests/main.nf.test.j2
+++ b/nf_core/module-template/tests/main.nf.test.j2
@@ -1,10 +1,15 @@
+{%- if not migrate_pytest_hard %}
 // TODO nf-core: Once you have added the required tests, please run the following command to build this file:
 // nf-core modules test {{ component_name }}
+{%- endif %}
 nextflow_process {
 
     name "Test Process {{ component_name_underscore|upper }}"
     script "../main.nf"
     process "{{ component_name_underscore|upper }}"
+    {%- if pytest_has_nextflow_config %}
+    config "./nextflow.config"
+    {%- endif %}
 
     tag "modules"
     tag "modules_{{ org_alphabet }}"
@@ -13,6 +18,7 @@ nextflow_process {
     {%- endif %}
     tag "{{ component_name }}"
 
+    {%- if not migrate_pytest_hard %}
     // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
     test("sarscov2 - bam") {
 
@@ -78,5 +84,9 @@ nextflow_process {
         }
 
     }
+    {%- endif %}
 
+{%- if migrate_pytest_hard %}
+{{ pytest_units_str }}
+{%- endif %}
 }
diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py
index a5e0795a9f..208b8bc667 100644
--- a/nf_core/modules/create.py
+++ b/nf_core/modules/create.py
@@ -18,6 +18,7 @@ def __init__(
         conda_version=None,
         empty_template=False,
         migrate_pytest=False,
+        migrate_pytest_hard=False,
     ):
         super().__init__(
             "modules",
@@ -31,4 +32,5 @@ def __init__(
             conda_version,
             empty_template,
             migrate_pytest,
+            migrate_pytest_hard,
         )