diff --git a/.editorconfig b/.editorconfig
index 449f446a3b..5aa8697d30 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -20,3 +20,11 @@ indent_style = unset
 
 [**/Makefile]
 indent_style = unset
+
+[tests/__snapshots__/*]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml
index 0bc5e432e7..9052c90ddc 100644
--- a/.github/actions/create-lint-wf/action.yml
+++ b/.github/actions/create-lint-wf/action.yml
@@ -27,7 +27,7 @@ runs:
       run: |
         mkdir -p create-lint-wf && cd create-lint-wf
         export NXF_WORK=$(pwd)
-        nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+        nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
     # Try syncing it before we change anything
     - name: nf-core sync
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 0de7287a57..4ae2714534 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -84,29 +84,29 @@ jobs:
         run: |
           mkdir create-test-lint-wf
           export NXF_WORK=$(pwd)
-          printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
+          printf "org: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > create-test-lint-wf/template_skip_all.yml
 
       - name: Create template skip github_badges
         run: |
-          printf "prefix: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
+          printf "org: my-prefix\nskip: github_badges" > create-test-lint-wf/template_skip_github_badges.yml
 
       - name: Create template skip igenomes
         run: |
-          printf "prefix: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
+          printf "org: my-prefix\nskip: igenomes" > create-test-lint-wf/template_skip_igenomes.yml
 
       - name: Create template skip ci
         run: |
-          printf "prefix: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
+          printf "org: my-prefix\nskip: ci" > create-test-lint-wf/template_skip_ci.yml
 
       - name: Create template skip nf_core_configs
         run: |
-          printf "prefix: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
+          printf "org: my-prefix\nskip: nf_core_configs" > create-test-lint-wf/template_skip_nf_core_configs.yml
 
       # Create a pipeline from the template
       - name: create a pipeline from the template ${{ matrix.TEMPLATE }}
         run: |
           cd create-test-lint-wf
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }}
 
       - name: run the pipeline
         run: |
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 87cdf2e7bb..a95a477459 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -70,7 +70,11 @@ jobs:
         run: |
           mkdir create-test-wf && cd create-test-wf
           export NXF_WORK=$(pwd)
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain
+          nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+          # echo current directory
+          pwd
+          # echo content of current directory
+          ls -la
           nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 70b9cfd0a8..4e873385e8 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -142,6 +142,13 @@ jobs:
             exit 1
           fi
 
+      - name: Store snapshot report
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        if: always()
+        with:
+          name: Snapshot Report ${{ matrix.test }}
+          path: ./snapshot_report.html
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
diff --git a/.gitignore b/.gitignore
index 271fdb14e3..a3721da86e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -115,3 +115,6 @@ ENV/
 pip-wheel-metadata
 .vscode
 .*.sw?
+
+# Textual
+snapshot_report.html
diff --git a/MANIFEST.in b/MANIFEST.in
index 5ec177b783..68f115d97f 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -9,3 +9,4 @@ include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
 include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
 include nf_core/assets/logo/placeholder_logo.svg
 include nf_core/assets/logo/MavenPro-Bold.ttf
+include nf_core/pipelines/create/create.tcss
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 147b0586b2..67af238b5c 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -17,7 +17,7 @@
 from nf_core.download import DownloadError
 from nf_core.modules.modules_repo import NF_CORE_MODULES_REMOTE
 from nf_core.params_file import ParamsFileBuilder
-from nf_core.utils import check_if_outdated, 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
@@ -45,7 +45,7 @@
         {
             "name": "Commands for developers",
             "commands": [
-                "create",
+                "pipelines",
                 "lint",
                 "modules",
                 "subworkflows",
@@ -56,6 +56,12 @@
             ],
         },
     ],
+    "nf-core pipelines": [
+        {
+            "name": "Pipeline commands",
+            "commands": ["create"],
+        },
+    ],
     "nf-core modules": [
         {
             "name": "For pipelines",
@@ -115,25 +121,11 @@ def run_nf_core():
     # print nf-core header if environment variable is not set
     if os.environ.get("_NF_CORE_COMPLETE") is None:
         # Print nf-core header
-        stderr.print(f"\n[green]{' ' * 42},--.[grey39]/[green],-.", highlight=False)
-        stderr.print(
-            "[blue]          ___     __   __   __   ___     [green]/,-._.--~\\",
-            highlight=False,
-        )
-        stderr.print(
-            r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {",
-            highlight=False,
-        )
-        stderr.print(
-            r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,",
-            highlight=False,
-        )
-        stderr.print(
-            "[green]                                          `._,._,'\n",
-            highlight=False,
-        )
+        stderr.print("\n")
+        for line in nfcore_logo:
+            stderr.print(line, highlight=False)
         stderr.print(
-            f"[grey39]    nf-core/tools version {__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
+            f"\n[grey39]    nf-core/tools version {__version__} - [link=https://nf-co.re]https://nf-co.re[/]",
             highlight=False,
         )
         try:
@@ -494,53 +486,6 @@ def licences(pipeline, json):
         sys.exit(1)
 
 
-# nf-core create
-@nf_core_cli.command()
-@click.option(
-    "-n",
-    "--name",
-    type=str,
-    help="The name of your new pipeline",
-)
-@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="1.0dev", 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("-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")
-def create(name, description, author, version, force, outdir, template_yaml, plain):
-    """
-    Create a new pipeline using the nf-core template.
-
-    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
-    files, boilerplate code and best-practices.
-    """
-    from nf_core.create import PipelineCreate
-
-    try:
-        create_obj = PipelineCreate(
-            name,
-            description,
-            author,
-            version=version,
-            force=force,
-            outdir=outdir,
-            template_yaml_path=template_yaml,
-            plain=plain,
-        )
-        create_obj.init_pipeline()
-    except UserWarning as e:
-        log.error(e)
-        sys.exit(1)
-
-
 # nf-core lint
 @nf_core_cli.command()
 @click.option(
@@ -658,6 +603,111 @@ def lint(
         sys.exit(1)
 
 
+# nf-core pipelines subcommands
+@nf_core_cli.group()
+@click.pass_context
+def pipelines(ctx):
+    """
+    Commands to manage nf-core pipelines.
+    """
+    # ensure that ctx.obj exists and is a dict (in case `cli()` is called
+    # by means other than the `if` block below)
+    ctx.ensure_object(dict)
+
+
+# nf-core pipelines create
+@pipelines.command("create")
+@click.pass_context
+@click.option(
+    "-n",
+    "--name",
+    type=str,
+    help="The name of your new pipeline",
+)
+@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("-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(
+    "--organisation",
+    type=str,
+    default="nf-core",
+    help="The name of the GitHub organisation where the pipeline will be hosted (default: nf-core)",
+)
+def create_pipeline(ctx, name, description, author, version, force, outdir, template_yaml, organisation):
+    """
+    Create a new pipeline using the nf-core template.
+
+    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
+    files, boilerplate code and best-practices.
+    \n\n
+    Run without any command line arguments to use an interactive interface.
+    """
+    from nf_core.pipelines.create import PipelineCreateApp
+    from nf_core.pipelines.create.create import PipelineCreate
+
+    if (name and description and author) or (template_yaml):
+        # If all command arguments are used, run without the interactive interface
+        try:
+            create_obj = PipelineCreate(
+                name,
+                description,
+                author,
+                version=version,
+                force=force,
+                outdir=outdir,
+                template_config=template_yaml,
+                organisation=organisation,
+            )
+            create_obj.init_pipeline()
+        except UserWarning as e:
+            log.error(e)
+            sys.exit(1)
+    elif name or description or author or version != "1.0.0dev" or force or outdir or organisation != "nf-core":
+        log.error(
+            "[red]Partial arguments supplied.[/] "
+            "Run without [i]any[/] arguments for an interactive interface, "
+            "or with at least name + description + author to use non-interactively."
+        )
+        sys.exit(1)
+    else:
+        log.info("Launching interactive nf-core pipeline creation tool.")
+        app = PipelineCreateApp()
+        app.run()
+        sys.exit(app.return_code or 0)
+
+
+# nf-core create (deprecated)
+@nf_core_cli.command(hidden=True, deprecated=True)
+@click.option(
+    "-n",
+    "--name",
+    type=str,
+    help="The name of your new pipeline",
+)
+@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, 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("-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")
+def create(name, description, author, version, force, outdir, template_yaml, plain):
+    """
+    DEPRECATED
+    Create a new pipeline using the nf-core template.
+
+    Uses the nf-core template to make a skeleton Nextflow pipeline with all required
+    files, boilerplate code and best-practices.
+    """
+    log.error(
+        "The `[magenta]nf-core create[/]` command is deprecated. Use `[magenta]nf-core pipelines create[/]` instead."
+    )
+    sys.exit(0)
+
+
 # nf-core modules subcommands
 @nf_core_cli.group()
 @click.option(
diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
index 014c2b5f09..fc044b6597 100644
--- a/nf_core/lint/files_unchanged.py
+++ b/nf_core/lint/files_unchanged.py
@@ -8,7 +8,7 @@
 
 import yaml
 
-import nf_core.create
+import nf_core.pipelines.create.create
 
 log = logging.getLogger(__name__)
 
@@ -109,7 +109,7 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
     ]
 
     # Only show error messages from pipeline creation
-    logging.getLogger("nf_core.create").setLevel(logging.ERROR)
+    logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
 
     # Generate a new pipeline with nf-core create that we can compare to
     tmp_dir = tempfile.mkdtemp()
@@ -119,16 +119,16 @@ def files_unchanged(self) -> Dict[str, Union[List[str], bool]]:
         "name": short_name,
         "description": self.nf_config["manifest.description"].strip("\"'"),
         "author": self.nf_config["manifest.author"].strip("\"'"),
-        "prefix": prefix,
+        "org": prefix,
     }
 
     template_yaml_path = Path(tmp_dir, "template.yaml")
     with open(template_yaml_path, "w") as fh:
         yaml.dump(template_yaml, fh, default_flow_style=False)
 
-    test_pipeline_dir = Path(tmp_dir, f"{prefix}-{short_name}")
-    create_obj = nf_core.create.PipelineCreate(
-        None, None, None, no_git=True, outdir=test_pipeline_dir, template_yaml_path=template_yaml_path
+    test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")
+    create_obj = nf_core.pipelines.create.create.PipelineCreate(
+        None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=template_yaml_path
     )
     create_obj.init_pipeline()
 
diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md
index 6244a6544e..3f541162d3 100644
--- a/nf_core/pipeline-template/.github/CONTRIBUTING.md
+++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md
@@ -9,7 +9,7 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 > [!NOTE]
 > If you need help using or modifying {{ name }} then the best place to ask is on the nf-core Slack [#{{ short_name }}](https://nfcore.slack.com/channels/{{ short_name }}) channel ([join our Slack here](https://nf-co.re/join/slack)).
@@ -63,7 +63,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 ## Getting help
 
diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
index 4f01a97993..9ad257a0b8 100644
--- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
+++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md
@@ -16,7 +16,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
-      {%- if branded %}
+      {%- if is_nfcore %}
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}
 - [ ] Make sure your code lints (`nf-core lint`).
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 88e0f1719f..e6351b0c6f 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -1,4 +1,4 @@
-{% if branded -%}
+{% if is_nfcore -%}
 
 <h1>
   <picture>
@@ -11,7 +11,7 @@
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/actions/workflows/ci.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/{{ name }}/actions/workflows/linting.yml/badge.svg)](https://github.com/{{ name }}/actions/workflows/linting.yml){% endif -%}
-{% if branded -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
+{% if is_nfcore -%}[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/{{ short_name }}/results){% endif -%}
 {%- if github_badges -%}
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
@@ -23,10 +23,10 @@
 [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/{{ name }})
 
 {% endif -%}
-{%- if branded -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
-{%- if branded -%}[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core){% endif -%}
-{%- if branded -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
-{%- if branded -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+{%- if is_nfcore -%}[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23{{ short_name }}-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/{{ short_name }}){% endif -%}
+{%- if is_nfcore -%}[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core){% endif -%}
+{%- if is_nfcore -%}[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core){% endif -%}
+{%- if is_nfcore -%}[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
 {% endif -%}
 
@@ -83,7 +83,7 @@ nextflow run {{ name }} \
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters).
 
@@ -107,7 +107,7 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-{% if branded -%}
+{% if is_nfcore -%}
 For further information or help, don't hesitate to get in touch on the [Slack `#{{ short_name }}` channel](https://nfcore.slack.com/channels/{{ short_name }}) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 {% endif -%}
@@ -121,7 +121,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-{% if branded -%}
+{% if is_nfcore -%}
 You can cite the `nf-core` publication as follows:
 
 {% else -%}
diff --git a/nf_core/pipeline-template/assets/email_template.txt b/nf_core/pipeline-template/assets/email_template.txt
index 25b12e8ce0..7927d45034 100644
--- a/nf_core/pipeline-template/assets/email_template.txt
+++ b/nf_core/pipeline-template/assets/email_template.txt
@@ -1,4 +1,4 @@
-{% if branded -%}
+{% if is_nfcore -%}
 ----------------------------------------------------
                                         ,--./,-.
         ___     __   __   __   ___     /,-._.--~\\
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index b13b7ae074..cd4e539b31 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -1,11 +1,11 @@
 report_comment: >
   {% if 'dev' in version -%}
   This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
-  analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
+  analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
   {%- else %}
   This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version }}" target="_blank">{{ name }}</a>
-  analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
+  analysis pipeline.{% if is_nfcore %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
   {% endif %}
 report_section_order:
diff --git a/nf_core/pipeline-template/docs/README.md b/nf_core/pipeline-template/docs/README.md
index e94889c53d..9a237c1ad4 100644
--- a/nf_core/pipeline-template/docs/README.md
+++ b/nf_core/pipeline-template/docs/README.md
@@ -6,7 +6,7 @@ The {{ name }} documentation is split into the following pages:
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
-    {%- if branded %}
+    {%- if is_nfcore %}
 
 You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
 {% else %}
diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md
index d46dfca04c..6645e0f6cf 100644
--- a/nf_core/pipeline-template/docs/usage.md
+++ b/nf_core/pipeline-template/docs/usage.md
@@ -1,6 +1,6 @@
 # {{ name }}: Usage
 
-{% if branded -%}
+{% if is_nfcore -%}
 
 ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/{{ short_name }}/usage](https://nf-co.re/{{ short_name }}/usage)
 
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 2590f7467b..1fd6a5b275 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -4,7 +4,7 @@
     {{ name }}
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Github : https://github.com/{{ name }}
-{%- if branded %}
+{%- if is_nfcore %}
     Website: https://nf-co.re/{{ short_name }}
     Slack  : https://nfcore.slack.com/channels/{{ short_name }}
 {%- endif %}
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index ae7c0b715f..18bad71b76 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -20,7 +20,7 @@
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.{% if branded %} See [usage docs](https://nf-co.re/{{ short_name }}/usage#samplesheet-input).{% endif %}",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.{% if is_nfcore %} See [usage docs](https://nf-co.re/{{ short_name }}/usage#samplesheet-input).{% endif %}",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
diff --git a/nf_core/pipelines/__init__.py b/nf_core/pipelines/__init__.py
new file mode 100644
index 0000000000..bc981c449f
--- /dev/null
+++ b/nf_core/pipelines/__init__.py
@@ -0,0 +1 @@
+from .create import PipelineCreateApp
diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py
new file mode 100644
index 0000000000..da6a693220
--- /dev/null
+++ b/nf_core/pipelines/create/__init__.py
@@ -0,0 +1,101 @@
+"""A Textual app to create a pipeline."""
+
+import logging
+
+from textual.app import App
+from textual.widgets import Button
+
+from nf_core.pipelines.create.basicdetails import BasicDetails
+from nf_core.pipelines.create.custompipeline import CustomPipeline
+from nf_core.pipelines.create.finaldetails import FinalDetails
+from nf_core.pipelines.create.githubexit import GithubExit
+from nf_core.pipelines.create.githubrepo import GithubRepo
+from nf_core.pipelines.create.githubrepoquestion import GithubRepoQuestion
+from nf_core.pipelines.create.loggingscreen import LoggingScreen
+from nf_core.pipelines.create.nfcorepipeline import NfcorePipeline
+from nf_core.pipelines.create.pipelinetype import ChoosePipelineType
+from nf_core.pipelines.create.utils import (
+    CreateConfig,
+    CustomLogHandler,
+    LoggingConsole,
+)
+from nf_core.pipelines.create.welcome import WelcomeScreen
+
+log_handler = CustomLogHandler(
+    console=LoggingConsole(classes="log_console"),
+    rich_tracebacks=True,
+    show_time=False,
+    show_path=False,
+    markup=True,
+)
+logging.basicConfig(
+    level="INFO",
+    handlers=[log_handler],
+    format="%(message)s",
+)
+log_handler.setLevel("INFO")
+
+
+class PipelineCreateApp(App[CreateConfig]):
+    """A Textual app to manage stopwatches."""
+
+    CSS_PATH = "create.tcss"
+    TITLE = "nf-core create"
+    SUB_TITLE = "Create a new pipeline with the nf-core pipeline template"
+    BINDINGS = [
+        ("d", "toggle_dark", "Toggle dark mode"),
+        ("q", "quit", "Quit"),
+    ]
+    SCREENS = {
+        "welcome": WelcomeScreen(),
+        "basic_details": BasicDetails(),
+        "choose_type": ChoosePipelineType(),
+        "type_custom": CustomPipeline(),
+        "type_nfcore": NfcorePipeline(),
+        "final_details": FinalDetails(),
+        "logging": LoggingScreen(),
+        "github_repo_question": GithubRepoQuestion(),
+        "github_repo": GithubRepo(),
+        "github_exit": GithubExit(),
+    }
+
+    # Initialise config as empty
+    TEMPLATE_CONFIG = CreateConfig()
+
+    # Initialise pipeline type
+    PIPELINE_TYPE = None
+
+    # Log handler
+    LOG_HANDLER = log_handler
+    # Logging state
+    LOGGING_STATE = None
+
+    def on_mount(self) -> None:
+        self.push_screen("welcome")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Handle all button pressed events."""
+        if event.button.id == "start":
+            self.push_screen("choose_type")
+        elif event.button.id == "type_nfcore":
+            self.PIPELINE_TYPE = "nfcore"
+            self.push_screen("basic_details")
+        elif event.button.id == "type_custom":
+            self.PIPELINE_TYPE = "custom"
+            self.push_screen("basic_details")
+        elif event.button.id == "continue":
+            self.push_screen("final_details")
+        elif event.button.id == "github_repo":
+            self.push_screen("github_repo")
+        elif event.button.id == "close_screen":
+            self.push_screen("github_repo_question")
+        elif event.button.id == "exit":
+            self.push_screen("github_exit")
+        if event.button.id == "close_app":
+            self.exit(return_code=0)
+        if event.button.id == "back":
+            self.pop_screen()
+
+    def action_toggle_dark(self) -> None:
+        """An action to toggle dark mode."""
+        self.dark: bool = not self.dark
diff --git a/nf_core/pipelines/create/basicdetails.py b/nf_core/pipelines/create/basicdetails.py
new file mode 100644
index 0000000000..b88ede10d0
--- /dev/null
+++ b/nf_core/pipelines/create/basicdetails.py
@@ -0,0 +1,110 @@
+"""A Textual app to create a pipeline."""
+
+from pathlib import Path
+from textwrap import dedent
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center, Horizontal
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Input, Markdown
+
+from nf_core.pipelines.create.utils import CreateConfig, TextInput, add_hide_class, remove_hide_class
+
+pipeline_exists_warn = """
+> ⚠️  **The pipeline you are trying to create already exists.**
+>
+> If you continue, you will **override** the existing pipeline.
+> Please change the pipeline or organisation name to create a different pipeline.
+"""
+
+
+class BasicDetails(Screen):
+    """Name, description, author, etc."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Basic details
+                """
+            )
+        )
+        with Horizontal():
+            yield TextInput(
+                "org",
+                "Organisation",
+                "GitHub organisation",
+                "nf-core",
+                classes="column",
+                disabled=self.parent.PIPELINE_TYPE == "nfcore",
+            )
+            yield TextInput(
+                "name",
+                "Pipeline Name",
+                "Workflow name",
+                classes="column",
+            )
+
+        yield TextInput(
+            "description",
+            "Description",
+            "A short description of your pipeline.",
+        )
+        yield TextInput(
+            "author",
+            "Author(s)",
+            "Name of the main author / authors",
+        )
+        yield Markdown(dedent(pipeline_exists_warn), id="exist_warn", classes="hide")
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Next", id="next", variant="success"),
+            classes="cta",
+        )
+
+    @on(Input.Changed)
+    @on(Input.Submitted)
+    def show_exists_warn(self):
+        """Check if the pipeline exists on every input change or submitted.
+        If the pipeline exists, show warning message saying that it will be overriden."""
+        config = {}
+        for text_input in self.query("TextInput"):
+            this_input = text_input.query_one(Input)
+            config[text_input.field_id] = this_input.value
+        if Path(config["org"] + "-" + config["name"]).is_dir():
+            remove_hide_class(self.parent, "exist_warn")
+        else:
+            add_hide_class(self.parent, "exist_warn")
+
+    def on_screen_resume(self):
+        """Hide warn message on screen resume.
+        Update displayed value on screen resume."""
+        add_hide_class(self.parent, "exist_warn")
+        for text_input in self.query("TextInput"):
+            if text_input.field_id == "org":
+                text_input.disabled = self.parent.PIPELINE_TYPE == "nfcore"
+
+    @on(Button.Pressed)
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Save fields to the config."""
+        config = {}
+        for text_input in self.query("TextInput"):
+            this_input = text_input.query_one(Input)
+            validation_result = this_input.validate(this_input.value)
+            config[text_input.field_id] = this_input.value
+            if not validation_result.is_valid:
+                text_input.query_one(".validation_msg").update("\n".join(validation_result.failure_descriptions))
+            else:
+                text_input.query_one(".validation_msg").update("")
+        try:
+            self.parent.TEMPLATE_CONFIG = CreateConfig(**config)
+            if event.button.id == "next":
+                if self.parent.PIPELINE_TYPE == "nfcore":
+                    self.parent.push_screen("type_nfcore")
+                elif self.parent.PIPELINE_TYPE == "custom":
+                    self.parent.push_screen("type_custom")
+        except ValueError:
+            pass
diff --git a/nf_core/create.py b/nf_core/pipelines/create/create.py
similarity index 62%
rename from nf_core/create.py
rename to nf_core/pipelines/create/create.py
index b420b1c86d..151ad83ff2 100644
--- a/nf_core/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -7,12 +7,11 @@
 import os
 import re
 import shutil
-import sys
 from pathlib import Path
+from typing import Optional, Union
 
 import git
 import jinja2
-import questionary
 import yaml
 
 import nf_core
@@ -20,6 +19,7 @@
 import nf_core.utils
 from nf_core.create_logo import create_logo
 from nf_core.lint_utils import run_prettier_on_file
+from nf_core.pipelines.create.utils import CreateConfig
 
 log = logging.getLogger(__name__)
 
@@ -31,31 +31,53 @@ class PipelineCreate:
         name (str): Name for the pipeline.
         description (str): Description for the pipeline.
         author (str): Authors name of the pipeline.
-        version (str): Version flag. Semantic versioning only. Defaults to `1.0dev`.
+        version (str): Version flag. Semantic versioning only. Defaults to `1.0.0dev`.
         no_git (bool): Prevents the creation of a local Git repository for the pipeline. Defaults to False.
-        force (bool): Overwrites a given workflow directory with the same name. Defaults to False.
+        force (bool): Overwrites a given workflow directory with the same name. Defaults to False. Used for tests and sync command.
             May the force be with you.
         outdir (str): Path to the local output directory.
-        template_yaml_path (str): Path to template.yml file for pipeline creation settings.
-        plain (bool): If true the Git repository will be initialized plain.
+        template_config (str|CreateConfig): Path to template.yml file for pipeline creation settings. or pydantic model with the customisation for pipeline creation settings.
+        organisation (str): Name of the GitHub organisation to create the pipeline. Will be the prefix of the pipeline.
+        from_config_file (bool): If true the pipeline will be created from the `.nf-core.yml` config file. Used for tests and sync command.
         default_branch (str): Specifies the --initial-branch name.
     """
 
     def __init__(
         self,
-        name,
-        description,
-        author,
-        version="1.0dev",
-        no_git=False,
-        force=False,
-        outdir=None,
-        template_yaml_path=None,
-        plain=False,
-        default_branch=None,
+        name: Optional[str] = None,
+        description: Optional[str] = None,
+        author: Optional[str] = None,
+        version: str = "1.0.0dev",
+        no_git: bool = False,
+        force: bool = False,
+        outdir: Optional[str] = None,
+        template_config: Optional[Union[str, CreateConfig, Path]] = None,
+        organisation: str = "nf-core",
+        from_config_file: bool = False,
+        default_branch: Optional[str] = None,
+        is_interactive: bool = False,
     ):
-        self.template_params, skip_paths_keys, self.template_yaml = self.create_param_dict(
-            name, description, author, version, template_yaml_path, plain, outdir if outdir else "."
+        if isinstance(template_config, CreateConfig):
+            self.config = template_config
+        elif from_config_file:
+            # Try reading config file
+            _, config_yml = nf_core.utils.load_tools_config(outdir if outdir else ".")
+            # Obtain a CreateConfig object from `.nf-core.yml` config file
+            if "template" in config_yml:
+                self.config = CreateConfig(**config_yml["template"])
+            else:
+                raise UserWarning("The template configuration was not provided in '.nf-core.yml'.")
+        elif (name and description and author) or (
+            template_config and (isinstance(template_config, str) or isinstance(template_config, Path))
+        ):
+            # Obtain a CreateConfig object from the template yaml file
+            self.config = self.check_template_yaml_info(template_config, name, description, author)
+            self.update_config(organisation, version, force, outdir)
+        else:
+            raise UserWarning("The template configuration was not provided.")
+
+        self.jinja_params, skip_paths = self.obtain_jinja_params_dict(
+            self.config.skip_features or [], self.config.outdir
         )
 
         skippable_paths = {
@@ -65,7 +87,7 @@ def __init__(
             ],
             "ci": [".github/workflows/"],
             "igenomes": ["conf/igenomes.config"],
-            "branded": [
+            "is_nfcore": [
                 ".github/ISSUE_TEMPLATE/config",
                 "CODE_OF_CONDUCT.md",
                 ".github/workflows/awsfulltest.yml",
@@ -73,176 +95,159 @@ def __init__(
             ],
         }
         # Get list of files we're skipping with the supplied skip keys
-        self.skip_paths = set(sp for k in skip_paths_keys for sp in skippable_paths[k])
+        self.skip_paths = set(sp for k in skip_paths for sp in skippable_paths[k])
 
         # Set convenience variables
-        self.name = self.template_params["name"]
+        self.name = self.config.name
 
         # Set fields used by the class methods
-        self.no_git = (
-            no_git if self.template_params["github"] else True
-        )  # Set to True if template was configured without github hosting
+        self.no_git = no_git
         self.default_branch = default_branch
-        self.force = force
-        if outdir is None:
-            outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
-        self.outdir = Path(outdir)
+        self.is_interactive = is_interactive
+        self.force = self.config.force
+        if self.config.outdir is None:
+            self.config.outdir = os.getcwd()
+        if self.config.outdir == ".":
+            self.outdir = Path(self.config.outdir, self.jinja_params["name_noslash"]).absolute()
+        else:
+            self.outdir = Path(self.config.outdir).absolute()
 
-    def create_param_dict(self, name, description, author, version, template_yaml_path, plain, pipeline_dir):
-        """Creates a dictionary of parameters for the new pipeline.
+    def check_template_yaml_info(self, template_yaml, name, description, author):
+        """Ensure that the provided template yaml file contains the necessary information.
 
         Args:
+            template_yaml (str): Template yaml file.
             name (str): Name for the pipeline.
             description (str): Description for the pipeline.
             author (str): Authors name of the pipeline.
-            version (str): Version flag.
-            template_yaml_path (str): Path to YAML file containing template parameters.
-            plain (bool): If true the pipeline template will be initialized plain, without customisation.
+
+        Returns:
+            CreateConfig: Pydantic model for the nf-core create config.
+
+        Raises:
+            UserWarning: if template yaml file does not contain all the necessary information.
+            UserWarning: if template yaml file does not exist.
+        """
+        # Obtain template customization info from template yaml file or `.nf-core.yml` config file
+        config = CreateConfig()
+        if template_yaml:
+            try:
+                with open(template_yaml) as f:
+                    template_yaml = yaml.safe_load(f)
+                    config = CreateConfig(**template_yaml)
+            except FileNotFoundError:
+                raise UserWarning(f"Template YAML file '{template_yaml}' not found.")
+
+        # Check required fields
+        missing_fields = []
+        if config.name is None and name is None:
+            missing_fields.append("name")
+        elif config.name is None:
+            config.name = name
+        if config.description is None and description is None:
+            missing_fields.append("description")
+        elif config.description is None:
+            config.description = description
+        if config.author is None and author is None:
+            missing_fields.append("author")
+        elif config.author is None:
+            config.author = author
+        if len(missing_fields) > 0:
+            raise UserWarning(
+                f"Template YAML file does not contain the following required fields: {', '.join(missing_fields)}"
+            )
+
+        return config
+
+    def update_config(self, organisation, version, force, outdir):
+        """Updates the config file with arguments provided through command line.
+
+        Args:
+            organisation (str): Name of the GitHub organisation to create the pipeline.
+            version (str): Version of the pipeline.
+            force (bool): Overwrites a given workflow directory with the same name.
+            outdir (str): Path to the local output directory.
+        """
+        if self.config.org is None:
+            self.config.org = organisation
+        if self.config.version is None:
+            self.config.version = version if version else "1.0.0dev"
+        if self.config.force is None:
+            self.config.force = force if force else False
+        if self.config.outdir is None:
+            self.config.outdir = outdir if outdir else "."
+        if self.config.is_nfcore is None:
+            self.config.is_nfcore = self.config.org == "nf-core"
+
+    def obtain_jinja_params_dict(self, features_to_skip, pipeline_dir):
+        """Creates a dictionary of parameters for the new pipeline.
+
+        Args:
+            features_to_skip (list<str>): List of template features/areas to skip.
             pipeline_dir (str): Path to the pipeline directory.
+
+        Returns:
+            jinja_params (dict): Dictionary of template areas to skip with values true/false.
+            skip_paths (list<str>): List of template areas which contain paths to skip.
         """
         # Try reading config file
         _, config_yml = nf_core.utils.load_tools_config(pipeline_dir)
 
-        # Obtain template customization info from template yaml file or `.nf-core.yml` config file
-        try:
-            if template_yaml_path is not None:
-                with open(template_yaml_path) as f:
-                    template_yaml = yaml.safe_load(f)
-            elif "template" in config_yml:
-                template_yaml = config_yml["template"]
-            else:
-                template_yaml = {}
-        except FileNotFoundError:
-            raise UserWarning(f"Template YAML file '{template_yaml_path}' not found.")
-
-        param_dict = {}
-        # Get the necessary parameters either from the template or command line arguments
-        param_dict["name"] = self.get_param("name", name, template_yaml, template_yaml_path)
-        param_dict["description"] = self.get_param("description", description, template_yaml, template_yaml_path)
-        param_dict["author"] = self.get_param("author", author, template_yaml, template_yaml_path)
-
-        if "version" in template_yaml:
-            if version is not None:
-                log.info(f"Overriding --version with version found in {template_yaml_path}")
-            version = template_yaml["version"]
-        param_dict["version"] = version
-
         # Define the different template areas, and what actions to take for each
         # if they are skipped
         template_areas = {
-            "github": {"name": "GitHub hosting", "file": True, "content": False},
-            "ci": {"name": "GitHub CI", "file": True, "content": False},
-            "github_badges": {"name": "GitHub badges", "file": False, "content": True},
-            "igenomes": {"name": "iGenomes config", "file": True, "content": True},
-            "nf_core_configs": {"name": "nf-core/configs", "file": False, "content": True},
+            "github": {"file": True, "content": False},
+            "ci": {"file": True, "content": False},
+            "github_badges": {"file": False, "content": True},
+            "igenomes": {"file": True, "content": True},
+            "nf_core_configs": {"file": False, "content": True},
         }
 
-        # Once all necessary parameters are set, check if the user wants to customize the template more
-        if template_yaml_path is None and not plain:
-            customize_template = questionary.confirm(
-                "Do you want to customize which parts of the template are used?",
-                style=nf_core.utils.nfcore_question_style,
-                default=False,
-            ).unsafe_ask()
-            if customize_template:
-                template_yaml.update(self.customize_template(template_areas))
-
-        # Now look in the template for more options, otherwise default to nf-core defaults
-        param_dict["prefix"] = template_yaml.get("prefix", "nf-core")
-        param_dict["branded"] = param_dict["prefix"] == "nf-core"
-
-        skip_paths = [] if param_dict["branded"] else ["branded"]
+        # Set the parameters for the jinja template
+        jinja_params = self.config.model_dump()
 
+        # Add template areas to jinja params and create list of areas with paths to skip
+        skip_paths = []
         for t_area in template_areas:
-            areas_to_skip = template_yaml.get("skip", [])
-            if isinstance(areas_to_skip, str):
-                areas_to_skip = [areas_to_skip]
-            if t_area in areas_to_skip:
+            if t_area in features_to_skip:
                 if template_areas[t_area]["file"]:
                     skip_paths.append(t_area)
-                param_dict[t_area] = False
+                jinja_params[t_area] = False
             else:
-                param_dict[t_area] = True
-        # If github is selected, exclude also github_badges
-        if not param_dict["github"]:
-            param_dict["github_badges"] = False
+                jinja_params[t_area] = True
+
+        # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files
+        if not jinja_params["is_nfcore"]:
+            skip_paths.append("is_nfcore")
 
         # Set the last parameters based on the ones provided
-        param_dict["short_name"] = (
-            param_dict["name"].lower().replace(r"/\s+/", "-").replace(f"{param_dict['prefix']}/", "").replace("/", "-")
+        jinja_params["short_name"] = (
+            jinja_params["name"].lower().replace(r"/\s+/", "-").replace(f"{jinja_params['org']}/", "").replace("/", "-")
         )
-        param_dict["name"] = f"{param_dict['prefix']}/{param_dict['short_name']}"
-        param_dict["name_noslash"] = param_dict["name"].replace("/", "-")
-        param_dict["prefix_nodash"] = param_dict["prefix"].replace("-", "")
-        param_dict["name_docker"] = param_dict["name"].replace(param_dict["prefix"], param_dict["prefix_nodash"])
-        param_dict["logo_light"] = f"nf-core-{param_dict['short_name']}_logo_light.png"
-        param_dict["logo_dark"] = f"nf-core-{param_dict['short_name']}_logo_dark.png"
-        param_dict["version"] = version
+        jinja_params["name"] = f"{jinja_params['org']}/{jinja_params['short_name']}"
+        jinja_params["name_noslash"] = jinja_params["name"].replace("/", "-")
+        jinja_params["prefix_nodash"] = jinja_params["org"].replace("-", "")
+        jinja_params["name_docker"] = jinja_params["name"].replace(jinja_params["org"], jinja_params["prefix_nodash"])
+        jinja_params["logo_light"] = f"{jinja_params['name_noslash']}_logo_light.png"
+        jinja_params["logo_dark"] = f"{jinja_params['name_noslash']}_logo_dark.png"
 
         if (
             "lint" in config_yml
             and "nextflow_config" in config_yml["lint"]
             and "manifest.name" in config_yml["lint"]["nextflow_config"]
         ):
-            return param_dict, skip_paths, template_yaml
+            return jinja_params, skip_paths
 
         # Check that the pipeline name matches the requirements
-        if not re.match(r"^[a-z]+$", param_dict["short_name"]):
-            if param_dict["prefix"] == "nf-core":
+        if not re.match(r"^[a-z]+$", jinja_params["short_name"]):
+            if jinja_params["is_nfcore"]:
                 raise UserWarning("[red]Invalid workflow name: must be lowercase without punctuation.")
             else:
                 log.warning(
                     "Your workflow name is not lowercase without punctuation. This may cause Nextflow errors.\nConsider changing the name to avoid special characters."
                 )
 
-        return param_dict, skip_paths, template_yaml
-
-    def customize_template(self, template_areas):
-        """Customizes the template parameters.
-
-        Args:
-            template_areas (list<str>): List of available template areas to skip.
-        """
-        template_yaml = {}
-        prefix = questionary.text("Pipeline prefix", style=nf_core.utils.nfcore_question_style).unsafe_ask()
-        while not re.match(r"^[a-zA-Z_][a-zA-Z0-9-_]*$", prefix):
-            log.error("[red]Pipeline prefix cannot start with digit or hyphen and cannot contain punctuation.[/red]")
-            prefix = questionary.text(
-                "Please provide a new pipeline prefix", style=nf_core.utils.nfcore_question_style
-            ).unsafe_ask()
-        template_yaml["prefix"] = prefix
-
-        choices = [{"name": template_areas[area]["name"], "value": area} for area in template_areas]
-        template_yaml["skip"] = questionary.checkbox(
-            "Skip template areas?", choices=choices, style=nf_core.utils.nfcore_question_style
-        ).unsafe_ask()
-        return template_yaml
-
-    def get_param(self, param_name, passed_value, template_yaml, template_yaml_path):
-        if param_name in template_yaml:
-            if passed_value is not None:
-                log.info(f"overriding --{param_name} with name found in {template_yaml_path}")
-            passed_value = template_yaml[param_name]
-        if passed_value is None:
-            passed_value = getattr(self, f"prompt_wf_{param_name}")()
-        return passed_value
-
-    def prompt_wf_name(self):
-        wf_name = questionary.text("Workflow name", style=nf_core.utils.nfcore_question_style).unsafe_ask()
-        while not re.match(r"^[a-z]+$", wf_name):
-            log.error("[red]Invalid workflow name: must be lowercase without punctuation.")
-            wf_name = questionary.text(
-                "Please provide a new workflow name", style=nf_core.utils.nfcore_question_style
-            ).unsafe_ask()
-        return wf_name
-
-    def prompt_wf_description(self):
-        wf_description = questionary.text("Description", style=nf_core.utils.nfcore_question_style).unsafe_ask()
-        return wf_description
-
-    def prompt_wf_author(self):
-        wf_author = questionary.text("Author", style=nf_core.utils.nfcore_question_style).unsafe_ask()
-        return wf_author
+        return jinja_params, skip_paths
 
     def init_pipeline(self):
         """Creates the nf-core pipeline."""
@@ -254,7 +259,7 @@ def init_pipeline(self):
         if not self.no_git:
             self.git_init_pipeline()
 
-        if self.template_params["branded"]:
+        if self.config.is_nfcore and not self.is_interactive:
             log.info(
                 "[green bold]!!!!!! IMPORTANT !!!!!!\n\n"
                 "[green not bold]If you are interested in adding your pipeline to the nf-core community,\n"
@@ -265,7 +270,7 @@ def init_pipeline(self):
 
     def render_template(self):
         """Runs Jinja to create a new nf-core pipeline."""
-        log.info(f"Creating new nf-core pipeline: '{self.name}'")
+        log.info(f"Creating new pipeline: '{self.name}'")
 
         # Check if the output directory exists
         if self.outdir.exists():
@@ -274,7 +279,7 @@ def render_template(self):
             else:
                 log.error(f"Output directory '{self.outdir}' exists!")
                 log.info("Use -f / --force to overwrite existing files")
-                sys.exit(1)
+                raise UserWarning(f"Output directory '{self.outdir}' exists!")
         else:
             os.makedirs(self.outdir)
 
@@ -282,15 +287,15 @@ def render_template(self):
         env = jinja2.Environment(
             loader=jinja2.PackageLoader("nf_core", "pipeline-template"), keep_trailing_newline=True
         )
-        template_dir = os.path.join(os.path.dirname(__file__), "pipeline-template")
-        object_attrs = self.template_params
+        template_dir = os.path.join(os.path.dirname(nf_core.__file__), "pipeline-template")
+        object_attrs = self.jinja_params
         object_attrs["nf_core_version"] = nf_core.__version__
 
         # Can't use glob.glob() as need recursive hidden dotfiles - https://stackoverflow.com/a/58126417/713980
         template_files = list(Path(template_dir).glob("**/*"))
         template_files += list(Path(template_dir).glob("*"))
         ignore_strs = [".pyc", "__pycache__", ".pyo", ".pyd", ".DS_Store", ".egg"]
-        short_name = self.template_params["short_name"]
+        short_name = self.jinja_params["short_name"]
         rename_files = {
             "workflows/pipeline.nf": f"workflows/{short_name}.nf",
             "subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf": f"subworkflows/local/utils_nfcore_{short_name}_pipeline/main.nf",
@@ -348,14 +353,14 @@ def render_template(self):
                 os.chmod(output_path, template_stat.st_mode)
 
         # Remove all unused parameters in the nextflow schema
-        if not self.template_params["igenomes"] or not self.template_params["nf_core_configs"]:
+        if not self.jinja_params["igenomes"] or not self.jinja_params["nf_core_configs"]:
             self.update_nextflow_schema()
 
-        if self.template_params["branded"]:
+        if self.config.is_nfcore:
             # Make a logo and save it, if it is a nf-core pipeline
             self.make_pipeline_logo()
         else:
-            if self.template_params["github"]:
+            if self.jinja_params["github"]:
                 # Remove field mentioning nf-core docs
                 # in the github bug report template
                 self.remove_nf_core_in_bug_report_template()
@@ -363,10 +368,10 @@ def render_template(self):
             # Update the .nf-core.yml with linting configurations
             self.fix_linting()
 
-        if self.template_yaml:
+        if self.config:
             config_fn, config_yml = nf_core.utils.load_tools_config(self.outdir)
-            with open(self.outdir / config_fn, "w") as fh:
-                config_yml.update(template=self.template_yaml)
+            with open(config_fn, "w") as fh:
+                config_yml.update(template=self.config.model_dump())
                 yaml.safe_dump(config_yml, fh)
                 log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
                 run_prettier_on_file(self.outdir / config_fn)
@@ -410,7 +415,7 @@ def fix_linting(self):
         for a customized pipeline.
         """
         # Create a lint config
-        short_name = self.template_params["short_name"]
+        short_name = self.jinja_params["short_name"]
         lint_config = {
             "files_exist": [
                 "CODE_OF_CONDUCT.md",
@@ -435,7 +440,7 @@ def fix_linting(self):
         }
 
         # Add GitHub hosting specific configurations
-        if not self.template_params["github"]:
+        if not self.jinja_params["github"]:
             lint_config["files_exist"].extend(
                 [
                     ".github/ISSUE_TEMPLATE/bug_report.yml",
@@ -461,7 +466,7 @@ def fix_linting(self):
             )
 
         # Add CI specific configurations
-        if not self.template_params["ci"]:
+        if not self.jinja_params["ci"]:
             lint_config["files_exist"].extend(
                 [
                     ".github/workflows/branch.yml",
@@ -472,7 +477,7 @@ def fix_linting(self):
             )
 
         # Add custom config specific configurations
-        if not self.template_params["nf_core_configs"]:
+        if not self.jinja_params["nf_core_configs"]:
             lint_config["files_exist"].extend(["conf/igenomes.config"])
             lint_config["nextflow_config"].extend(
                 [
@@ -484,15 +489,15 @@ def fix_linting(self):
             )
 
         # Add igenomes specific configurations
-        if not self.template_params["igenomes"]:
+        if not self.jinja_params["igenomes"]:
             lint_config["files_exist"].extend(["conf/igenomes.config"])
 
         # Add github badges specific configurations
-        if not self.template_params["github_badges"] or not self.template_params["github"]:
+        if not self.jinja_params["github_badges"] or not self.jinja_params["github"]:
             lint_config["readme"] = ["nextflow_badge"]
 
-        # If the pipeline is unbranded
-        if not self.template_params["branded"]:
+        # If the pipeline is not nf-core
+        if not self.config.is_nfcore:
             lint_config["files_unchanged"].extend([".github/ISSUE_TEMPLATE/bug_report.yml"])
 
         # Add the lint content to the preexisting nf-core config
@@ -506,11 +511,11 @@ def fix_linting(self):
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"
-        create_logo(text=self.template_params["short_name"], dir=email_logo_path, theme="light", force=self.force)
+        create_logo(text=self.jinja_params["short_name"], dir=email_logo_path, theme="light", force=self.force)
         for theme in ["dark", "light"]:
             readme_logo_path = Path(self.outdir) / "docs" / "images"
             create_logo(
-                text=self.template_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force
+                text=self.jinja_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force
             )
 
     def git_init_pipeline(self):
@@ -534,7 +539,7 @@ def git_init_pipeline(self):
                 "Pipeline git repository will not be initialised."
             )
 
-        log.info("Initialising pipeline git repository")
+        log.info("Initialising local pipeline git repository")
         repo = git.Repo.init(self.outdir)
         repo.git.add(A=True)
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
@@ -554,14 +559,16 @@ def git_init_pipeline(self):
                     repo.git.branch("TEMPLATE")
                     repo.git.branch("dev")
                 else:
-                    log.error(
+                    raise UserWarning(
                         "Branches 'TEMPLATE' and 'dev' already exist. Use --force to overwrite existing branches."
                     )
-                    sys.exit(1)
-        log.info(
-            "Done. Remember to add a remote and push to GitHub:\n"
-            f"[white on grey23] cd {self.outdir} \n"
-            " git remote add origin git@github.com:USERNAME/REPO_NAME.git \n"
-            " git push --all origin                                       "
-        )
-        log.info("This will also push your newly created dev branch and the TEMPLATE branch for syncing.")
+        if self.is_interactive:
+            log.info(f"Pipeline created: ./{self.outdir.relative_to(Path.cwd())}")
+        else:
+            log.info(
+                "Done. Remember to add a remote and push to GitHub:\n"
+                f"[white on grey23] cd {self.outdir} \n"
+                " git remote add origin git@github.com:USERNAME/REPO_NAME.git \n"
+                " git push --all origin                                       "
+            )
+            log.info("This will also push your newly created dev branch and the TEMPLATE branch for syncing.")
diff --git a/nf_core/pipelines/create/create.tcss b/nf_core/pipelines/create/create.tcss
new file mode 100644
index 0000000000..67394a9de3
--- /dev/null
+++ b/nf_core/pipelines/create/create.tcss
@@ -0,0 +1,135 @@
+#logo {
+    width: 100%;
+    content-align-horizontal: center;
+    content-align-vertical: middle;
+}
+.cta {
+    layout: horizontal;
+    margin-bottom: 1;
+}
+.cta Button {
+    margin: 0 3;
+}
+
+.pipeline-type-grid {
+    height: auto;
+    margin-bottom: 2;
+}
+
+.custom_grid {
+    height: auto;
+}
+.custom_grid Switch {
+    width: auto;
+}
+.custom_grid Static {
+    width: 1fr;
+    margin: 1 8;
+}
+.custom_grid Button {
+    width: auto;
+}
+
+.field_help {
+    padding: 1 1 0 1;
+    color: $text-muted;
+    text-style: italic;
+}
+.validation_msg {
+    padding: 0 1;
+    color: $error;
+}
+.-valid {
+    border: tall $success-darken-3;
+}
+
+Horizontal{
+    width: 100%;
+    height: auto;
+}
+.column {
+    width: 1fr;
+}
+
+HorizontalScroll {
+    width: 100%;
+}
+.feature_subtitle {
+    color: grey;
+}
+
+Vertical{
+    height: auto;
+}
+
+.features-container {
+    padding: 0 4 1 4;
+}
+
+/* Display help messages */
+
+.help_box {
+    background: #333333;
+    padding: 1 3 0 3;
+    margin: 0 5 2 5;
+    overflow-y: auto;
+    transition: height 50ms;
+    display: none;
+    height: 0;
+}
+.displayed .help_box {
+    display: block;
+    height: 12;
+}
+#show_help {
+    display: block;
+}
+#hide_help {
+    display: none;
+}
+.displayed #show_help {
+    display: none;
+}
+.displayed #hide_help {
+    display: block;
+}
+
+/* Show password */
+
+#show_password {
+    display: block;
+}
+#hide_password {
+    display: none;
+}
+.displayed #show_password {
+    display: none;
+}
+.displayed #hide_password {
+    display: block;
+}
+
+/* Logging console */
+
+.log_console {
+    height: auto;
+    background: #333333;
+    padding: 1 3;
+    margin: 0 4 2 4;
+}
+
+.hide {
+    display: none;
+}
+
+/* Layouts */
+.col-2 {
+    grid-size: 2 1;
+}
+
+.ghrepo-cols {
+    margin: 0 4;
+}
+.ghrepo-cols Button {
+    margin-top: 2;
+}
diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py
new file mode 100644
index 0000000000..7d460db65d
--- /dev/null
+++ b/nf_core/pipelines/create/custompipeline.py
@@ -0,0 +1,99 @@
+from textwrap import dedent
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center, ScrollableContainer
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown, Switch
+
+from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes
+
+markdown_ci = """
+Nf-core provides a set of Continuous Integration (CI) tests for Github.
+When you open a pull request (PR) on your pipeline repository, these tests will run automatically.
+
+There are different types of tests:
+* Linting tests check that your code is formatted correctly and that it adheres to nf-core standards
+    For code linting they will use [prettier](https://prettier.io/).
+* Pipeline tests run your pipeline on a small dataset to check that it works
+    These tests are run with a small test dataset on GitHub and a larger test dataset on AWS
+* Marking old issues as stale
+"""
+
+markdown_badges = """
+The pipeline `README.md` will include badges for:
+* AWS CI Tests
+* Zenodo DOI
+* Nextflow
+* Conda
+* Docker
+* Singularity
+* Launching on Nextflow Tower
+"""
+
+markdown_configuration = """
+Nf-core has a repository with a collection of configuration profiles.
+
+Those config files define a set of parameters which are specific to compute environments at different Institutions.
+They can be used within all nf-core pipelines.
+If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation.
+
+For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)
+"""
+
+
+class CustomPipeline(Screen):
+    """Select if the pipeline will use genomic data."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Template features
+                """
+            )
+        )
+        yield ScrollableContainer(
+            PipelineFeature(
+                markdown_genomes,
+                "Use reference genomes",
+                "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes",
+                "igenomes",
+            ),
+            PipelineFeature(
+                markdown_ci,
+                "Add Github CI tests",
+                "The pipeline will include several GitHub actions for Continuous Integration (CI) testing",
+                "ci",
+            ),
+            PipelineFeature(
+                markdown_badges,
+                "Add Github badges",
+                "The README.md file of the pipeline will include GitHub badges",
+                "github_badges",
+            ),
+            PipelineFeature(
+                markdown_configuration,
+                "Add configuration files",
+                "The pipeline will include configuration profiles containing custom parameters requried to run nf-core pipelines at different institutions",
+                "nf_core_configs",
+            ),
+            classes="features-container",
+        )
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Continue", id="continue", variant="success"),
+            classes="cta",
+        )
+
+    @on(Button.Pressed, "#continue")
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Save fields to the config."""
+        skip = []
+        for feature_input in self.query("PipelineFeature"):
+            this_switch = feature_input.query_one(Switch)
+            if not this_switch.value:
+                skip.append(this_switch.id)
+        self.parent.TEMPLATE_CONFIG.__dict__.update({"skip_features": skip, "is_nfcore": False})
diff --git a/nf_core/pipelines/create/finaldetails.py b/nf_core/pipelines/create/finaldetails.py
new file mode 100644
index 0000000000..bd15cf9ddd
--- /dev/null
+++ b/nf_core/pipelines/create/finaldetails.py
@@ -0,0 +1,110 @@
+"""A Textual app to create a pipeline."""
+
+from pathlib import Path
+from textwrap import dedent
+
+from textual import on, work
+from textual.app import ComposeResult
+from textual.containers import Center, Horizontal
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Input, Markdown
+
+from nf_core.pipelines.create.create import PipelineCreate
+from nf_core.pipelines.create.utils import ShowLogs, TextInput, add_hide_class, remove_hide_class
+
+pipeline_exists_warn = """
+> ⚠️  **The pipeline you are trying to create already exists.**
+>
+> If you continue, you will **override** the existing pipeline.
+> Please change the pipeline or organisation name to create a different pipeline.
+> Alternatively, provide a different output directory.
+"""
+
+
+class FinalDetails(Screen):
+    """Name, description, author, etc."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Final details
+                """
+            )
+        )
+
+        with Horizontal():
+            yield TextInput(
+                "version",
+                "Version",
+                "First version of the pipeline",
+                "1.0.0dev",
+                classes="column",
+            )
+            yield TextInput(
+                "outdir",
+                "Output directory",
+                "Path to the output directory where the pipeline will be created",
+                ".",
+                classes="column",
+            )
+
+        yield Markdown(dedent(pipeline_exists_warn), id="exist_warn", classes="hide")
+
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Finish", id="finish", variant="success"),
+            classes="cta",
+        )
+
+    @on(Button.Pressed, "#finish")
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Save fields to the config."""
+        new_config = {}
+        for text_input in self.query("TextInput"):
+            this_input = text_input.query_one(Input)
+            validation_result = this_input.validate(this_input.value)
+            new_config[text_input.field_id] = this_input.value
+            if not validation_result.is_valid:
+                text_input.query_one(".validation_msg").update("\n".join(validation_result.failure_descriptions))
+            else:
+                text_input.query_one(".validation_msg").update("")
+        try:
+            self.parent.TEMPLATE_CONFIG.__dict__.update(new_config)
+        except ValueError:
+            pass
+
+        # Create the new pipeline
+        self._create_pipeline()
+        self.parent.LOGGING_STATE = "pipeline created"
+        self.parent.push_screen("logging")
+
+    @on(Input.Changed)
+    @on(Input.Submitted)
+    def show_exists_warn(self):
+        """Check if the pipeline exists on every input change or submitted.
+        If the pipeline exists, show warning message saying that it will be overriden."""
+        outdir = ""
+        for text_input in self.query("TextInput"):
+            this_input = text_input.query_one(Input)
+            if text_input.field_id == "outdir":
+                outdir = this_input.value
+        if Path(outdir, self.parent.TEMPLATE_CONFIG.org + "-" + self.parent.TEMPLATE_CONFIG.name).is_dir():
+            remove_hide_class(self.parent, "exist_warn")
+
+    def on_screen_resume(self):
+        """Hide warn message on screen resume."""
+        add_hide_class(self.parent, "exist_warn")
+
+    @work(thread=True, exclusive=True)
+    def _create_pipeline(self) -> None:
+        """Create the pipeline."""
+        self.post_message(ShowLogs())
+        create_obj = PipelineCreate(
+            template_config=self.parent.TEMPLATE_CONFIG,
+            is_interactive=True,
+        )
+        create_obj.init_pipeline()
+        remove_hide_class(self.parent, "close_screen")
diff --git a/nf_core/pipelines/create/githubexit.py b/nf_core/pipelines/create/githubexit.py
new file mode 100644
index 0000000000..3dac88cc5f
--- /dev/null
+++ b/nf_core/pipelines/create/githubexit.py
@@ -0,0 +1,48 @@
+from textwrap import dedent
+
+from textual.app import ComposeResult
+from textual.containers import Center
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown, Static
+
+from nf_core.utils import nfcore_logo
+
+exit_help_text_markdown = """
+If you would like to create the GitHub repository later, you can do it manually by following these steps:
+
+1. Create a new GitHub repository
+2. Add the remote to your local repository:
+    ```bash
+    cd <pipeline_directory>
+    git remote add origin git@github.com:<username>/<repo_name>.git
+    ```
+3. Push the code to the remote:
+    ```bash
+    git push --all origin
+    ```
+    > 💡 Note the `--all` flag: this is needed to push all branches to the remote.
+"""
+
+
+class GithubExit(Screen):
+    """A screen to show a help text when a GitHub repo is NOT created."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # HowTo create a GitHub repository
+                """
+            )
+        )
+        yield Static(
+            "\n" + "\n".join(nfcore_logo) + "\n",
+            id="logo",
+        )
+        yield Markdown(exit_help_text_markdown)
+        yield Center(
+            Button("Close", id="close_app", variant="success"),
+            classes="cta",
+        )
diff --git a/nf_core/pipelines/create/githubrepo.py b/nf_core/pipelines/create/githubrepo.py
new file mode 100644
index 0000000000..99e7b09ab8
--- /dev/null
+++ b/nf_core/pipelines/create/githubrepo.py
@@ -0,0 +1,253 @@
+import logging
+import os
+from pathlib import Path
+from textwrap import dedent
+
+import git
+import yaml
+from github import Github, GithubException, UnknownObjectException
+from textual import on, work
+from textual.app import ComposeResult
+from textual.containers import Center, Horizontal, Vertical
+from textual.message import Message
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Input, Markdown, Static, Switch
+
+from nf_core.pipelines.create.utils import ShowLogs, TextInput, remove_hide_class
+
+log = logging.getLogger(__name__)
+
+github_org_help = """
+> ⚠️  **You can't create a repository directly in the nf-core organisation.**
+>
+> Please create the pipeline repo to an organisation where you have access or use your user account.
+> A core-team member will be able to transfer the repo to nf-core once the development has started.
+
+> 💡 Your GitHub user account will be used by default if `nf-core` is given as the org name.
+"""
+
+
+class GithubRepo(Screen):
+    """Create a GitHub repository and push all branches."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        gh_user, gh_token = self._get_github_credentials()
+        github_text_markdown = dedent(
+            """
+            # Create GitHub repository
+
+            Now that we have created a new pipeline locally, we can
+            create a new GitHub repository and push the code to it.
+            """
+        )
+        if gh_user:
+            github_text_markdown += f">\n> 💡 _Found GitHub username {'and token ' if gh_token else ''}in local [GitHub CLI](https://cli.github.com/) config_\n>\n"
+        yield Markdown(github_text_markdown)
+        with Horizontal(classes="ghrepo-cols"):
+            yield TextInput(
+                "gh_username",
+                "GitHub username",
+                "Your GitHub username",
+                default=gh_user[0] if gh_user is not None else "GitHub username",
+                classes="column",
+            )
+            yield TextInput(
+                "token",
+                "GitHub token",
+                "Your GitHub [link=https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens]personal access token[/link] for login.",
+                default=gh_token if gh_token is not None else "GitHub token",
+                password=True,
+                classes="column",
+            )
+            yield Button("Show", id="show_password")
+            yield Button("Hide", id="hide_password")
+        with Horizontal(classes="ghrepo-cols"):
+            yield TextInput(
+                "repo_org",
+                "Organisation name",
+                "The name of the organisation where the GitHub repo will be cretaed",
+                default=self.parent.TEMPLATE_CONFIG.org,
+                classes="column",
+            )
+            yield TextInput(
+                "repo_name",
+                "Repository name",
+                "The name of the new GitHub repository",
+                default=self.parent.TEMPLATE_CONFIG.name,
+                classes="column",
+            )
+        if self.parent.TEMPLATE_CONFIG.is_nfcore:
+            yield Markdown(dedent(github_org_help))
+        with Horizontal(classes="ghrepo-cols"):
+            yield Switch(value=False, id="private")
+            with Vertical():
+                yield Static("Private", classes="")
+                yield Static("Select to make the new GitHub repo private.", classes="feature_subtitle")
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Create GitHub repo", id="create_github", variant="success"),
+            Button("Finish without creating a repo", id="exit", variant="primary"),
+            classes="cta",
+        )
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Create a GitHub repo or show help message and exit"""
+        if event.button.id == "show_password":
+            self.add_class("displayed")
+            text_input = self.query_one("#token", TextInput)
+            text_input.query_one(Input).password = False
+        elif event.button.id == "hide_password":
+            self.remove_class("displayed")
+            text_input = self.query_one("#token", TextInput)
+            text_input.query_one(Input).password = True
+        elif event.button.id == "create_github":
+            # Create a GitHub repo
+
+            # Save GitHub username, token and repo name
+            github_variables = {}
+            for text_input in self.query("TextInput"):
+                this_input = text_input.query_one(Input)
+                github_variables[text_input.field_id] = this_input.value
+            # Save GitHub repo config
+            for switch_input in self.query("Switch"):
+                github_variables[switch_input.id] = switch_input.value
+
+            # Pipeline git repo
+            pipeline_repo = git.Repo.init(
+                Path(self.parent.TEMPLATE_CONFIG.outdir)
+                / Path(self.parent.TEMPLATE_CONFIG.org + "-" + self.parent.TEMPLATE_CONFIG.name)
+            )
+
+            # GitHub authentication
+            if github_variables["token"]:
+                github_auth = self._github_authentication(github_variables["gh_username"], github_variables["token"])
+            else:
+                raise UserWarning(
+                    f"Could not authenticate to GitHub with user name '{github_variables['gh_username']}'."
+                    "Please provide an authentication token or set the environment variable 'GITHUB_AUTH_TOKEN'."
+                )
+
+            user = github_auth.get_user()
+            org = None
+            # Make sure that the authentication was successful
+            try:
+                user.login
+                log.debug("GitHub authentication successful")
+            except GithubException:
+                raise UserWarning(
+                    f"Could not authenticate to GitHub with user name '{github_variables['gh_username']}'."
+                    "Please make sure that the provided user name and token are correct."
+                )
+
+            # Check if organisation exists
+            # If the organisation is nf-core or it doesn't exist, the repo will be created in the user account
+            if github_variables["repo_org"] != "nf-core":
+                try:
+                    org = github_auth.get_organization(github_variables["repo_org"])
+                    log.info(
+                        f"Repo will be created in the GitHub organisation account '{github_variables['repo_org']}'"
+                    )
+                except UnknownObjectException:
+                    log.warn(f"Provided organisation '{github_variables['repo_org']}' not found. ")
+
+            # Create the repo
+            try:
+                if org:
+                    self._create_repo_and_push(
+                        org,
+                        github_variables["repo_name"],
+                        pipeline_repo,
+                        github_variables["private"],
+                    )
+                else:
+                    # Create the repo in the user's account
+                    log.info(
+                        f"Repo will be created in the GitHub organisation account '{github_variables['gh_username']}'"
+                    )
+                    self._create_repo_and_push(
+                        user,
+                        github_variables["repo_name"],
+                        pipeline_repo,
+                        github_variables["private"],
+                    )
+            except UserWarning as e:
+                log.error(f"There was an error with message: {e}")
+                self.parent.push_screen("github_exit")
+
+            self.parent.LOGGING_STATE = "repo created"
+            self.parent.push_screen("logging")
+
+    class RepoExists(Message):
+        """Custom message to indicate that the GitHub repo already exists."""
+
+        pass
+
+    @on(RepoExists)
+    def show_github_info_button(self) -> None:
+        remove_hide_class(self.parent, "exit")
+        remove_hide_class(self.parent, "back")
+
+    @work(thread=True, exclusive=True)
+    def _create_repo_and_push(self, org, repo_name, pipeline_repo, private):
+        """Create a GitHub repository and push all branches."""
+        self.post_message(ShowLogs())
+        # Check if repo already exists
+        try:
+            repo = org.get_repo(repo_name)
+            # Check if it has a commit history
+            try:
+                repo.get_commits().totalCount
+                raise UserWarning(f"GitHub repository '{repo_name}' already exists")
+            except GithubException:
+                # Repo is empty
+                repo_exists = True
+            except UserWarning as e:
+                # Repo already exists
+                log.error(e)
+                self.post_message(self.RepoExists())
+                return
+        except UnknownObjectException:
+            # Repo doesn't exist
+            repo_exists = False
+
+        # Create the repo
+        if not repo_exists:
+            repo = org.create_repo(repo_name, description=self.parent.TEMPLATE_CONFIG.description, private=private)
+            log.info(f"GitHub repository '{repo_name}' created successfully")
+            remove_hide_class(self.parent, "close_app")
+
+        # Add the remote
+        try:
+            pipeline_repo.create_remote("origin", repo.clone_url)
+        except git.exc.GitCommandError:
+            # Remote already exists
+            pass
+        # Push all branches
+        pipeline_repo.remotes.origin.push(all=True).raise_if_error()
+
+    def _github_authentication(self, gh_username, gh_token):
+        """Authenticate to GitHub"""
+        log.debug(f"Authenticating GitHub as {gh_username}")
+        github_auth = Github(gh_username, gh_token)
+        return github_auth
+
+    def _get_github_credentials(self):
+        """Get GitHub credentials"""
+        gh_user = None
+        gh_token = None
+        # Use gh CLI config if installed
+        gh_cli_config_fn = os.path.expanduser("~/.config/gh/hosts.yml")
+        if os.path.exists(gh_cli_config_fn):
+            try:
+                with open(gh_cli_config_fn) as fh:
+                    gh_cli_config = yaml.safe_load(fh)
+                    gh_user = (gh_cli_config["github.com"]["user"],)
+                    gh_token = gh_cli_config["github.com"]["oauth_token"]
+            except KeyError:
+                pass
+        # If gh CLI not installed, try to get credentials from environment variables
+        elif os.environ.get("GITHUB_TOKEN") is not None:
+            gh_token = self.auth = os.environ["GITHUB_TOKEN"]
+        return (gh_user, gh_token)
diff --git a/nf_core/pipelines/create/githubrepoquestion.py b/nf_core/pipelines/create/githubrepoquestion.py
new file mode 100644
index 0000000000..ded33d188a
--- /dev/null
+++ b/nf_core/pipelines/create/githubrepoquestion.py
@@ -0,0 +1,36 @@
+import logging
+from textwrap import dedent
+
+from textual.app import ComposeResult
+from textual.containers import Center
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown
+
+log = logging.getLogger(__name__)
+
+github_text_markdown = """
+After creating the pipeline template locally, we can create a GitHub repository and push the code to it.
+
+Do you want to create a GitHub repository?
+"""
+
+
+class GithubRepoQuestion(Screen):
+    """Ask if the user wants to create a GitHub repository."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Create GitHub repository
+                """
+            )
+        )
+        yield Markdown(dedent(github_text_markdown))
+        yield Center(
+            Button("Create GitHub repo", id="github_repo", variant="success"),
+            Button("Finish without creating a repo", id="exit", variant="primary"),
+            classes="cta",
+        )
diff --git a/nf_core/pipelines/create/loggingscreen.py b/nf_core/pipelines/create/loggingscreen.py
new file mode 100644
index 0000000000..f862dccea1
--- /dev/null
+++ b/nf_core/pipelines/create/loggingscreen.py
@@ -0,0 +1,48 @@
+from textwrap import dedent
+
+from textual.app import ComposeResult
+from textual.containers import Center
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown, Static
+
+from nf_core.pipelines.create.utils import add_hide_class
+from nf_core.utils import nfcore_logo
+
+
+class LoggingScreen(Screen):
+    """A screen to show the final logs."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Logging
+                """
+            )
+        )
+        yield Static(
+            "\n" + "\n".join(nfcore_logo) + "\n",
+            id="logo",
+        )
+        yield Markdown("Creating...")
+        yield Center(self.parent.LOG_HANDLER.console)
+        yield Center(
+            Button("Back", id="back", variant="default", classes="hide"),
+            Button("Continue", id="close_screen", variant="success", classes="hide"),
+            Button("Continue", id="exit", variant="success", classes="hide"),
+            Button("Close App", id="close_app", variant="success", classes="hide"),
+            classes="cta",
+        )
+
+    def on_screen_resume(self):
+        """Hide all buttons as disabled on screen resume."""
+        button_ids = ["back", "close_screen", "exit", "close_app"]
+        for button in self.query("Button"):
+            if button.id in button_ids:
+                add_hide_class(self.parent, button.id)
+
+    def on_screen_suspend(self):
+        """Clear console on screen suspend."""
+        self.parent.LOG_HANDLER.console.clear()
diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py
new file mode 100644
index 0000000000..49cc1f8f86
--- /dev/null
+++ b/nf_core/pipelines/create/nfcorepipeline.py
@@ -0,0 +1,48 @@
+from textwrap import dedent
+
+from textual import on
+from textual.app import ComposeResult
+from textual.containers import Center, ScrollableContainer
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown, Switch
+
+from nf_core.pipelines.create.utils import PipelineFeature, markdown_genomes
+
+
+class NfcorePipeline(Screen):
+    """Select if the pipeline will use genomic data."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(
+            dedent(
+                """
+                # Template features
+                """
+            )
+        )
+        yield ScrollableContainer(
+            PipelineFeature(
+                markdown_genomes,
+                "Use reference genomes",
+                "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes",
+                "igenomes",
+            ),
+            classes="features-container",
+        )
+        yield Center(
+            Button("Back", id="back", variant="default"),
+            Button("Continue", id="continue", variant="success"),
+            classes="cta",
+        )
+
+    @on(Button.Pressed, "#continue")
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """Save fields to the config."""
+        skip = []
+        for feature_input in self.query("PipelineFeature"):
+            this_switch = feature_input.query_one(Switch)
+            if not this_switch.value:
+                skip.append(this_switch.id)
+        self.parent.TEMPLATE_CONFIG.__dict__.update({"skip_features": skip, "is_nfcore": True})
diff --git a/nf_core/pipelines/create/pipelinetype.py b/nf_core/pipelines/create/pipelinetype.py
new file mode 100644
index 0000000000..48914e8555
--- /dev/null
+++ b/nf_core/pipelines/create/pipelinetype.py
@@ -0,0 +1,56 @@
+from textual.app import ComposeResult
+from textual.containers import Center, Grid
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown
+
+markdown_intro = """
+# Choose pipeline type
+"""
+
+markdown_type_nfcore = """
+## Choose _"nf-core"_ if:
+
+* You want your pipeline to be part of the nf-core community
+* You think that there's an outside chance that it ever _could_ be part of nf-core
+"""
+markdown_type_custom = """
+## Choose _"Custom"_ if:
+
+* Your pipeline will _never_ be part of nf-core
+* You want full control over *all* features that are included from the template
+      (including those that are mandatory for nf-core).
+"""
+
+markdown_details = """
+## What's the difference?
+
+Choosing _"nf-core"_ effectively pre-selects the following template features:
+
+* GitHub Actions continuous-integration configuration files:
+    * Pipeline test runs: Small-scale (GitHub) and large-scale (AWS)
+    * Code formatting checks with [Prettier](https://prettier.io/)
+    * Auto-fix linting functionality using [@nf-core-bot](https://github.com/nf-core-bot)
+    * Marking old issues as stale
+* Inclusion of [shared nf-core configuration profiles](https://nf-co.re/configs)
+"""
+
+
+class ChoosePipelineType(Screen):
+    """Choose whether this will be an nf-core pipeline or not."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Markdown(markdown_intro)
+        yield Grid(
+            Center(
+                Markdown(markdown_type_nfcore),
+                Center(Button("nf-core", id="type_nfcore", variant="success")),
+            ),
+            Center(
+                Markdown(markdown_type_custom),
+                Center(Button("Custom", id="type_custom", variant="primary")),
+            ),
+            classes="col-2 pipeline-type-grid",
+        )
+        yield Markdown(markdown_details)
diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py
new file mode 100644
index 0000000000..6006452baf
--- /dev/null
+++ b/nf_core/pipelines/create/utils.py
@@ -0,0 +1,226 @@
+import re
+from logging import LogRecord
+from pathlib import Path
+from typing import Optional, Union
+
+from pydantic import BaseModel, ConfigDict, ValidationError, field_validator
+from rich.logging import RichHandler
+from textual import on
+from textual._context import active_app
+from textual.app import ComposeResult
+from textual.containers import HorizontalScroll
+from textual.message import Message
+from textual.validation import ValidationResult, Validator
+from textual.widget import Widget
+from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch
+
+
+class CreateConfig(BaseModel):
+    """Pydantic model for the nf-core create config."""
+
+    org: Optional[str] = None
+    name: Optional[str] = None
+    description: Optional[str] = None
+    author: Optional[str] = None
+    version: Optional[str] = None
+    force: Optional[bool] = True
+    outdir: Optional[str] = None
+    skip_features: Optional[list] = None
+    is_nfcore: Optional[bool] = None
+
+    model_config = ConfigDict(extra="allow")
+
+    @field_validator("name")
+    @classmethod
+    def name_nospecialchars(cls, v: str) -> str:
+        """Check that the pipeline name is simple."""
+        if not re.match(r"^[a-z]+$", v):
+            raise ValueError("Must be lowercase without punctuation.")
+        return v
+
+    @field_validator("org", "description", "author", "version", "outdir")
+    @classmethod
+    def notempty(cls, v: str) -> str:
+        """Check that string values are not empty."""
+        if v.strip() == "":
+            raise ValueError("Cannot be left empty.")
+        return v
+
+    @field_validator("version")
+    @classmethod
+    def version_nospecialchars(cls, v: str) -> str:
+        """Check that the pipeline version is simple."""
+        if not re.match(r"^([0-9]+)(\.?([0-9]+))*(dev)?$", v):
+            raise ValueError(
+                "Must contain at least one number, and can be prefixed by 'dev'. Do not use a 'v' prefix or spaces."
+            )
+        return v
+
+    @field_validator("outdir")
+    @classmethod
+    def path_valid(cls, v: str) -> str:
+        """Check that a path is valid."""
+        if not Path(v).is_dir():
+            raise ValueError("Must be a valid path.")
+        return v
+
+
+class TextInput(Static):
+    """Widget for text inputs.
+
+    Provides standard interface for a text input with help text
+    and validation messages.
+    """
+
+    def __init__(self, field_id, placeholder, description, default=None, password=None, **kwargs) -> None:
+        """Initialise the widget with our values.
+
+        Pass on kwargs upstream for standard usage."""
+        super().__init__(**kwargs)
+        self.field_id: str = field_id
+        self.id: str = field_id
+        self.placeholder: str = placeholder
+        self.description: str = description
+        self.default: str = default
+        self.password: bool = password
+
+    def compose(self) -> ComposeResult:
+        yield Static(self.description, classes="field_help")
+        yield Input(
+            placeholder=self.placeholder,
+            validators=[ValidateConfig(self.field_id)],
+            value=self.default,
+            password=self.password,
+        )
+        yield Static(classes="validation_msg")
+
+    @on(Input.Changed)
+    @on(Input.Submitted)
+    def show_invalid_reasons(self, event: Union[Input.Changed, Input.Submitted]) -> None:
+        """Validate the text input and show errors if invalid."""
+        if not event.validation_result.is_valid:
+            self.query_one(".validation_msg").update("\n".join(event.validation_result.failure_descriptions))
+        else:
+            self.query_one(".validation_msg").update("")
+
+
+class ValidateConfig(Validator):
+    """Validate any config value, using Pydantic."""
+
+    def __init__(self, key) -> None:
+        """Initialise the validator with the model key to validate."""
+        super().__init__()
+        self.key = key
+
+    def validate(self, value: str) -> ValidationResult:
+        """Try creating a Pydantic object with this key set to this value.
+
+        If it fails, return the error messages."""
+        try:
+            CreateConfig(**{f"{self.key}": value})
+            return self.success()
+        except ValidationError as e:
+            return self.failure(", ".join([err["msg"] for err in e.errors()]))
+
+
+class HelpText(Markdown):
+    """A class to show a text box with help text."""
+
+    def __init__(self, **kwargs) -> None:
+        super().__init__(**kwargs)
+
+    def show(self) -> None:
+        """Method to show the help text box."""
+        self.add_class("displayed")
+
+    def hide(self) -> None:
+        """Method to hide the help text box."""
+        self.remove_class("displayed")
+
+
+class PipelineFeature(Static):
+    """Widget for the selection of pipeline features."""
+
+    def __init__(self, markdown: str, title: str, subtitle: str, field_id: str, **kwargs) -> None:
+        super().__init__(**kwargs)
+        self.markdown = markdown
+        self.title = title
+        self.subtitle = subtitle
+        self.field_id = field_id
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        """When the button is pressed, change the type of the button."""
+        if event.button.id == "show_help":
+            self.add_class("displayed")
+        elif event.button.id == "hide_help":
+            self.remove_class("displayed")
+
+    def compose(self) -> ComposeResult:
+        """
+        Create child widgets.
+
+        Displayed row with a switch, a short text description and a help button.
+        Hidden row with a help text box.
+        """
+        yield HorizontalScroll(
+            Switch(value=True, id=self.field_id),
+            Static(self.title, classes="feature_title"),
+            Static(self.subtitle, classes="feature_subtitle"),
+            Button("Show help", id="show_help", variant="primary"),
+            Button("Hide help", id="hide_help"),
+            classes="custom_grid",
+        )
+        yield HelpText(markdown=self.markdown, classes="help_box")
+
+
+class LoggingConsole(RichLog):
+    file = False
+    console: Widget
+
+    def print(self, content):
+        self.write(content)
+
+
+class CustomLogHandler(RichHandler):
+    """A Logging handler which extends RichHandler to write to a Widget and handle a Textual App."""
+
+    def emit(self, record: LogRecord) -> None:
+        """Invoked by logging."""
+        try:
+            _app = active_app.get()
+        except LookupError:
+            pass
+        else:
+            super().emit(record)
+
+
+class ShowLogs(Message):
+    """Custom message to show the logging messages."""
+
+    pass
+
+
+## Functions
+def add_hide_class(app, widget_id: str) -> None:
+    """Add class 'hide' to a widget. Not display widget."""
+    app.get_widget_by_id(widget_id).add_class("hide")
+
+
+def remove_hide_class(app, widget_id: str) -> None:
+    """Remove class 'hide' to a widget. Display widget."""
+    app.get_widget_by_id(widget_id).remove_class("hide")
+
+
+## Markdown text to reuse in different screens
+markdown_genomes = """
+Nf-core pipelines are configured to use a copy of the most common reference genome files.
+
+By selecting this option, your pipeline will include a configuration file specifying the paths to these files.
+
+The required code to use these files will also be included in the template.
+When the pipeline user provides an appropriate genome key,
+the pipeline will automatically download the required reference files.
+
+For more information about reference genomes in nf-core pipelines,
+see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes).
+"""
diff --git a/nf_core/pipelines/create/welcome.py b/nf_core/pipelines/create/welcome.py
new file mode 100644
index 0000000000..1da0a3c01d
--- /dev/null
+++ b/nf_core/pipelines/create/welcome.py
@@ -0,0 +1,37 @@
+from textual.app import ComposeResult
+from textual.containers import Center
+from textual.screen import Screen
+from textual.widgets import Button, Footer, Header, Markdown, Static
+
+from nf_core.utils import nfcore_logo
+
+markdown = """
+# Welcome to the nf-core pipeline creation wizard
+
+This app will help you create a new Nextflow pipeline
+from the [nf-core/tools pipeline template](https://github.com/nf-core/tools).
+
+The template helps anyone benefit from nf-core best practices,
+and is a requirement for nf-core pipelines.
+
+> 💡 If you want to add a pipeline to nf-core, please
+> [join on Slack](https://nf-co.re/join) and discuss your plans with the
+> community as early as possible; _**ideally before you start on your pipeline!**_
+> See the [nf-core guidelines](https://nf-co.re/docs/contributing/guidelines)
+> and the [#new-pipelines](https://nfcore.slack.com/channels/new-pipelines)
+> Slack channel for more information.
+"""
+
+
+class WelcomeScreen(Screen):
+    """A welcome screen for the app."""
+
+    def compose(self) -> ComposeResult:
+        yield Header()
+        yield Footer()
+        yield Static(
+            "\n" + "\n".join(nfcore_logo) + "\n",
+            id="logo",
+        )
+        yield Markdown(markdown)
+        yield Center(Button("Let's go!", id="start", variant="success"), classes="cta")
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 5e7b198d8d..81082c24be 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -15,8 +15,8 @@
 from git import GitCommandError, InvalidGitRepositoryError
 
 import nf_core
-import nf_core.create
 import nf_core.list
+import nf_core.pipelines.create.create
 import nf_core.utils
 
 log = logging.getLogger(__name__)
@@ -257,7 +257,7 @@ def make_template_pipeline(self):
         log.info("Making a new template pipeline using pipeline variables")
 
         # Only show error messages from pipeline creation
-        logging.getLogger("nf_core.create").setLevel(logging.ERROR)
+        logging.getLogger("nf_core.pipelines.create").setLevel(logging.ERROR)
 
         # Re-write the template yaml info from .nf-core.yml config
         if "template" in self.config_yml:
@@ -265,7 +265,7 @@ def make_template_pipeline(self):
                 yaml.safe_dump(self.config_yml, config_path)
 
         try:
-            nf_core.create.PipelineCreate(
+            nf_core.pipelines.create.create.PipelineCreate(
                 name=self.wf_config["manifest.name"].strip('"').strip("'"),
                 description=self.wf_config["manifest.description"].strip('"').strip("'"),
                 version=self.wf_config["manifest.version"].strip('"').strip("'"),
@@ -273,7 +273,6 @@ def make_template_pipeline(self):
                 force=True,
                 outdir=self.pipeline_dir,
                 author=self.wf_config["manifest.author"].strip('"').strip("'"),
-                plain=True,
             ).init_pipeline()
         except Exception as err:
             # Reset to where you were to prevent git getting messed up.
diff --git a/nf_core/utils.py b/nf_core/utils.py
index 5b31f48f4b..8c50f0a49f 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -36,6 +36,15 @@
 
 log = logging.getLogger(__name__)
 
+# ASCII nf-core logo
+nfcore_logo = [
+    r"[green]                                          ,--.[grey39]/[green],-.",
+    r"[blue]          ___     __   __   __   ___     [green]/,-._.--~\ ",
+    r"[blue]    |\ | |__  __ /  ` /  \ |__) |__      [yellow]   }  {",
+    r"[blue]    | \| |       \__, \__/ |  \ |___     [green]\`-._,-`-,",
+    r"[green]                                          `._,._,'",
+]
+
 # Custom style for questionary
 nfcore_question_style = prompt_toolkit.styles.Style(
     [
diff --git a/pytest.ini b/pytest.ini
index cf37159478..fcbd03fa45 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -2,3 +2,6 @@
 testpaths =
     tests
 python_files = test_*.py
+
+# automatically run coroutine tests with asyncio
+asyncio_mode = auto
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 9fbb49c10c..fa98655aed 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -6,8 +6,14 @@ responses
 ruff
 Sphinx
 sphinx-rtd-theme
+textual-dev>=1.2.1
+mypy
+types-PyYAML
+types-requests
 types-jsonschema
 types-Markdown
 types-PyYAML
 types-requests
 types-setuptools
+pytest-textual-snapshot
+ruff
diff --git a/requirements.txt b/requirements.txt
index 6b5b3ab57d..acf30f491d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,7 @@
 click
 filetype
 GitPython
+PyGithub
 jinja2
 jsonschema>=3.0
 markdown>=3.3
@@ -9,6 +10,7 @@ pillow
 pdiff
 pre-commit
 prompt_toolkit>=3.0.3
+pydantic>=2.2.1
 pytest-workflow>=2.0.0
 pytest>=7.0.0
 pyyaml
@@ -19,4 +21,6 @@ requests_cache
 rich-click>=1.6.1
 rich>=13.3.1
 tabulate
+textual>=0.47.1
 trogon
+pdiff
diff --git a/tests/__snapshots__/test_create_app.ambr b/tests/__snapshots__/test_create_app.ambr
new file mode 100644
index 0000000000..c486ec4f8f
--- /dev/null
+++ b/tests/__snapshots__/test_create_app.ambr
@@ -0,0 +1,3329 @@
+# serializer version: 1
+# name: test_basic_details_custom
+  '''
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+  
+  '''
+# ---
+# name: test_basic_details_nfcore
+  '''
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+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_choose_type
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
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+          font-family: Fira Code, monospace;
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+          font-variant-east-asian: full-width;
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+  .terminal-3444045345-r17 { fill: #001541 }
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+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_customisation_help
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
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+          font-weight: 700;
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+          font-variant-east-asian: full-width;
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+          font-weight: bold;
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+  .terminal-3071202289-r6 { fill: #0053aa }
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+  .terminal-3071202289-r8 { fill: #1e1e1e }
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+  .terminal-3071202289-r22 { fill: #008139 }
+  .terminal-3071202289-r23 { fill: #ddedf9 }
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+  </svg>
+  
+  '''
+# ---
+# name: test_final_details
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
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+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_github_details
+  '''
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+      <!-- Generated with Rich https://www.textualize.io -->
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+          font-variant-east-asian: full-width;
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+          font-weight: bold;
+          font-family: arial;
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+  .terminal-436990287-r6 { fill: #0053aa }
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+  .terminal-436990287-r8 { fill: #a5a5a5;font-style: italic; }
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+  .terminal-436990287-r16 { fill: #b93c5b }
+  .terminal-436990287-r17 { fill: #4ebf71 }
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+  .terminal-436990287-r19 { fill: #969696;font-weight: bold }
+  .terminal-436990287-r20 { fill: #808080 }
+  .terminal-436990287-r21 { fill: #7ae998 }
+  .terminal-436990287-r22 { fill: #507bb3 }
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+  .terminal-436990287-r24 { fill: #dde6ed;font-weight: bold }
+  .terminal-436990287-r25 { fill: #001541 }
+  .terminal-436990287-r26 { fill: #ddedf9 }
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+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_github_exit_message
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
+  
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Regular"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Regular.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Regular.woff") format("woff");
+          font-style: normal;
+          font-weight: 400;
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+  </text><text class="terminal-2484211597-r8" x="292.8" y="312.8" textLength="610" clip-path="url(#terminal-2484211597-line-12)">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;`._,._,&#x27;</text><text class="terminal-2484211597-r1" x="1220" y="312.8" textLength="12.2" clip-path="url(#terminal-2484211597-line-12)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="337.2" textLength="12.2" clip-path="url(#terminal-2484211597-line-13)">
+  </text><text class="terminal-2484211597-r4" x="48.8" y="361.6" textLength="1122.4" clip-path="url(#terminal-2484211597-line-14)">If&#160;you&#160;would&#160;like&#160;to&#160;create&#160;the&#160;GitHub&#160;repository&#160;later,&#160;you&#160;can&#160;do&#160;it&#160;manually&#160;by&#160;following</text><text class="terminal-2484211597-r1" x="1220" y="361.6" textLength="12.2" clip-path="url(#terminal-2484211597-line-14)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="410.4" textLength="12.2" clip-path="url(#terminal-2484211597-line-16)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="508" textLength="12.2" clip-path="url(#terminal-2484211597-line-20)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="581.2" textLength="12.2" clip-path="url(#terminal-2484211597-line-23)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="605.6" textLength="12.2" clip-path="url(#terminal-2484211597-line-24)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="727.6" textLength="12.2" clip-path="url(#terminal-2484211597-line-29)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="752" textLength="12.2" clip-path="url(#terminal-2484211597-line-30)">
+  </text><text class="terminal-2484211597-r16" x="97.6" y="776.4" textLength="12.2" clip-path="url(#terminal-2484211597-line-31)">▌</text><text class="terminal-2484211597-r17" x="122" y="776.4" textLength="134.2" clip-path="url(#terminal-2484211597-line-31)">💡&#160;Note&#160;the&#160;</text><text class="terminal-2484211597-r18" x="268.4" y="776.4" textLength="61" clip-path="url(#terminal-2484211597-line-31)">--all</text><text class="terminal-2484211597-r17" x="329.4" y="776.4" textLength="695.4" clip-path="url(#terminal-2484211597-line-31)">&#160;flag:&#160;this&#160;is&#160;needed&#160;to&#160;push&#160;all&#160;branches&#160;to&#160;the&#160;remote.</text><text class="terminal-2484211597-r1" x="1220" y="776.4" textLength="12.2" clip-path="url(#terminal-2484211597-line-31)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="825.2" textLength="12.2" clip-path="url(#terminal-2484211597-line-33)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="849.6" textLength="12.2" clip-path="url(#terminal-2484211597-line-34)">
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+  </text><text class="terminal-2484211597-r12" x="524.6" y="898.4" textLength="61" clip-path="url(#terminal-2484211597-line-36)">Close</text><text class="terminal-2484211597-r1" x="1220" y="898.4" textLength="12.2" clip-path="url(#terminal-2484211597-line-36)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="947.2" textLength="12.2" clip-path="url(#terminal-2484211597-line-38)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="971.6" textLength="12.2" clip-path="url(#terminal-2484211597-line-39)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="1044.8" textLength="12.2" clip-path="url(#terminal-2484211597-line-42)">
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+  </text><text class="terminal-2484211597-r1" x="1220" y="1142.4" textLength="12.2" clip-path="url(#terminal-2484211597-line-46)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="1166.8" textLength="12.2" clip-path="url(#terminal-2484211597-line-47)">
+  </text><text class="terminal-2484211597-r1" x="1220" y="1191.2" textLength="12.2" clip-path="url(#terminal-2484211597-line-48)">
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+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_github_question
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
+  
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Regular"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Regular.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Regular.woff") format("woff");
+          font-style: normal;
+          font-weight: 400;
+      }
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Bold"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Bold.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Bold.woff") format("woff");
+          font-style: bold;
+          font-weight: 700;
+      }
+  
+      .terminal-4165331380-matrix {
+          font-family: Fira Code, monospace;
+          font-size: 20px;
+          line-height: 24.4px;
+          font-variant-east-asian: full-width;
+      }
+  
+      .terminal-4165331380-title {
+          font-size: 18px;
+          font-weight: bold;
+          font-family: arial;
+      }
+  
+      .terminal-4165331380-r1 { fill: #c5c8c6 }
+  .terminal-4165331380-r2 { fill: #e3e3e3 }
+  .terminal-4165331380-r3 { fill: #989898 }
+  .terminal-4165331380-r4 { fill: #e1e1e1 }
+  .terminal-4165331380-r5 { fill: #121212 }
+  .terminal-4165331380-r6 { fill: #0053aa }
+  .terminal-4165331380-r7 { fill: #dde8f3;font-weight: bold }
+  .terminal-4165331380-r8 { fill: #7ae998 }
+  .terminal-4165331380-r9 { fill: #507bb3 }
+  .terminal-4165331380-r10 { fill: #4ebf71;font-weight: bold }
+  .terminal-4165331380-r11 { fill: #dde6ed;font-weight: bold }
+  .terminal-4165331380-r12 { fill: #008139 }
+  .terminal-4165331380-r13 { fill: #001541 }
+  .terminal-4165331380-r14 { fill: #ddedf9 }
+      </style>
+  
+      <defs>
+      <clipPath id="terminal-4165331380-clip-terminal">
+        <rect x="0" y="0" width="1219.0" height="1219.0" />
+      </clipPath>
+      <clipPath id="terminal-4165331380-line-0">
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-4">
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-6">
+      <rect x="0" y="147.9" width="1220" height="24.65"/>
+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-8">
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-9">
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-10">
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+              </clipPath>
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+      <rect x="0" y="318.7" width="1220" height="24.65"/>
+              </clipPath>
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+              </clipPath>
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+      <rect x="0" y="367.5" width="1220" height="24.65"/>
+              </clipPath>
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+              </clipPath>
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+      <rect x="0" y="416.3" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-4165331380-line-18">
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-19">
+      <rect x="0" y="465.1" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-4165331380-line-20">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-4165331380-line-26">
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+              </clipPath>
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+              </clipPath>
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+      <rect x="0" y="684.7" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-4165331380-line-29">
+      <rect x="0" y="709.1" width="1220" height="24.65"/>
+              </clipPath>
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+      <rect x="0" y="733.5" width="1220" height="24.65"/>
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+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_type_custom
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
+  
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Regular"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Regular.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Regular.woff") format("woff");
+          font-style: normal;
+          font-weight: 400;
+      }
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Bold"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Bold.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Bold.woff") format("woff");
+          font-style: bold;
+          font-weight: 700;
+      }
+  
+      .terminal-3459022791-matrix {
+          font-family: Fira Code, monospace;
+          font-size: 20px;
+          line-height: 24.4px;
+          font-variant-east-asian: full-width;
+      }
+  
+      .terminal-3459022791-title {
+          font-size: 18px;
+          font-weight: bold;
+          font-family: arial;
+      }
+  
+      .terminal-3459022791-r1 { fill: #c5c8c6 }
+  .terminal-3459022791-r2 { fill: #e3e3e3 }
+  .terminal-3459022791-r3 { fill: #989898 }
+  .terminal-3459022791-r4 { fill: #e1e1e1 }
+  .terminal-3459022791-r5 { fill: #121212 }
+  .terminal-3459022791-r6 { fill: #0053aa }
+  .terminal-3459022791-r7 { fill: #dde8f3;font-weight: bold }
+  .terminal-3459022791-r8 { fill: #1e1e1e }
+  .terminal-3459022791-r9 { fill: #507bb3 }
+  .terminal-3459022791-r10 { fill: #e2e2e2 }
+  .terminal-3459022791-r11 { fill: #808080 }
+  .terminal-3459022791-r12 { fill: #dde6ed;font-weight: bold }
+  .terminal-3459022791-r13 { fill: #001541 }
+  .terminal-3459022791-r14 { fill: #454a50 }
+  .terminal-3459022791-r15 { fill: #7ae998 }
+  .terminal-3459022791-r16 { fill: #e2e3e3;font-weight: bold }
+  .terminal-3459022791-r17 { fill: #0a180e;font-weight: bold }
+  .terminal-3459022791-r18 { fill: #000000 }
+  .terminal-3459022791-r19 { fill: #008139 }
+  .terminal-3459022791-r20 { fill: #ddedf9 }
+      </style>
+  
+      <defs>
+      <clipPath id="terminal-3459022791-clip-terminal">
+        <rect x="0" y="0" width="1219.0" height="1219.0" />
+      </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-1">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-2">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-3">
+      <rect x="0" y="74.7" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-4">
+      <rect x="0" y="99.1" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-5">
+      <rect x="0" y="123.5" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-6">
+      <rect x="0" y="147.9" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-7">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-8">
+      <rect x="0" y="196.7" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-9">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-10">
+      <rect x="0" y="245.5" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-11">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-15">
+      <rect x="0" y="367.5" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-16">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-17">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-18">
+      <rect x="0" y="440.7" width="1220" height="24.65"/>
+              </clipPath>
+  <clipPath id="terminal-3459022791-line-19">
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-20">
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-22">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-31">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-38">
+      <rect x="0" y="928.7" width="1220" height="24.65"/>
+              </clipPath>
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+              </clipPath>
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+      <rect x="0" y="977.5" width="1220" height="24.65"/>
+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-3459022791-line-48">
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+              </clipPath>
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+  '''
+# ---
+# name: test_type_nfcore
+  '''
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+# ---
+# name: test_type_nfcore_validation
+  '''
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+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
+# name: test_welcome
+  '''
+  <svg class="rich-terminal" viewBox="0 0 1238 1270.0" xmlns="http://www.w3.org/2000/svg">
+      <!-- Generated with Rich https://www.textualize.io -->
+      <style>
+  
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Regular"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff2/FiraCode-Regular.woff2") format("woff2"),
+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Regular.woff") format("woff");
+          font-style: normal;
+          font-weight: 400;
+      }
+      @font-face {
+          font-family: "Fira Code";
+          src: local("FiraCode-Bold"),
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+                  url("https://cdnjs.cloudflare.com/ajax/libs/firacode/6.2.0/woff/FiraCode-Bold.woff") format("woff");
+          font-style: bold;
+          font-weight: 700;
+      }
+  
+      .terminal-1144763792-matrix {
+          font-family: Fira Code, monospace;
+          font-size: 20px;
+          line-height: 24.4px;
+          font-variant-east-asian: full-width;
+      }
+  
+      .terminal-1144763792-title {
+          font-size: 18px;
+          font-weight: bold;
+          font-family: arial;
+      }
+  
+      .terminal-1144763792-r1 { fill: #c5c8c6 }
+  .terminal-1144763792-r2 { fill: #e3e3e3 }
+  .terminal-1144763792-r3 { fill: #989898 }
+  .terminal-1144763792-r4 { fill: #98e024 }
+  .terminal-1144763792-r5 { fill: #626262 }
+  .terminal-1144763792-r6 { fill: #9d65ff }
+  .terminal-1144763792-r7 { fill: #fd971f }
+  .terminal-1144763792-r8 { fill: #e1e1e1 }
+  .terminal-1144763792-r9 { fill: #121212 }
+  .terminal-1144763792-r10 { fill: #0053aa }
+  .terminal-1144763792-r11 { fill: #dde8f3;font-weight: bold }
+  .terminal-1144763792-r12 { fill: #e1e1e1;text-decoration: underline; }
+  .terminal-1144763792-r13 { fill: #4ebf71 }
+  .terminal-1144763792-r14 { fill: #e2e2e2 }
+  .terminal-1144763792-r15 { fill: #e2e2e2;text-decoration: underline; }
+  .terminal-1144763792-r16 { fill: #e2e2e2;font-weight: bold;font-style: italic; }
+  .terminal-1144763792-r17 { fill: #7ae998 }
+  .terminal-1144763792-r18 { fill: #4ebf71;font-weight: bold }
+  .terminal-1144763792-r19 { fill: #008139 }
+  .terminal-1144763792-r20 { fill: #ddedf9 }
+      </style>
+  
+      <defs>
+      <clipPath id="terminal-1144763792-clip-terminal">
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+      </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-1144763792-line-3">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
+  <clipPath id="terminal-1144763792-line-38">
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+              </clipPath>
+  <clipPath id="terminal-1144763792-line-39">
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+              </clipPath>
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+  </text><text class="terminal-1144763792-r9" x="48.8" y="312.8" textLength="12.2" clip-path="url(#terminal-1144763792-line-12)">▔</text><text class="terminal-1144763792-r9" x="61" y="312.8" textLength="1098" clip-path="url(#terminal-1144763792-line-12)">▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔</text><text class="terminal-1144763792-r9" x="1159" y="312.8" textLength="12.2" clip-path="url(#terminal-1144763792-line-12)">▔</text><text class="terminal-1144763792-r1" x="1220" y="312.8" textLength="12.2" clip-path="url(#terminal-1144763792-line-12)">
+  </text><text class="terminal-1144763792-r8" x="48.8" y="337.2" textLength="768.6" clip-path="url(#terminal-1144763792-line-13)">This&#160;app&#160;will&#160;help&#160;you&#160;create&#160;a&#160;new&#160;Nextflow&#160;pipeline&#160;from&#160;the&#160;</text><text class="terminal-1144763792-r12" x="817.4" y="337.2" textLength="280.6" clip-path="url(#terminal-1144763792-line-13)">nf-core/tools&#160;pipeline&#160;</text><text class="terminal-1144763792-r1" x="1220" y="337.2" textLength="12.2" clip-path="url(#terminal-1144763792-line-13)">
+  </text><text class="terminal-1144763792-r12" x="48.8" y="361.6" textLength="97.6" clip-path="url(#terminal-1144763792-line-14)">template</text><text class="terminal-1144763792-r8" x="146.4" y="361.6" textLength="12.2" clip-path="url(#terminal-1144763792-line-14)">.</text><text class="terminal-1144763792-r1" x="1220" y="361.6" textLength="12.2" clip-path="url(#terminal-1144763792-line-14)">
+  </text><text class="terminal-1144763792-r1" x="1220" y="386" textLength="12.2" clip-path="url(#terminal-1144763792-line-15)">
+  </text><text class="terminal-1144763792-r8" x="48.8" y="410.4" textLength="1073.6" clip-path="url(#terminal-1144763792-line-16)">The&#160;template&#160;helps&#160;anyone&#160;benefit&#160;from&#160;nf-core&#160;best&#160;practices,&#160;and&#160;is&#160;a&#160;requirement&#160;for&#160;</text><text class="terminal-1144763792-r1" x="1220" y="410.4" textLength="12.2" clip-path="url(#terminal-1144763792-line-16)">
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+  </text><text class="terminal-1144763792-r1" x="1220" y="459.2" textLength="12.2" clip-path="url(#terminal-1144763792-line-18)">
+  </text><text class="terminal-1144763792-r13" x="48.8" y="483.6" textLength="12.2" clip-path="url(#terminal-1144763792-line-19)">▌</text><text class="terminal-1144763792-r14" x="73.2" y="483.6" textLength="622.2" clip-path="url(#terminal-1144763792-line-19)">💡&#160;If&#160;you&#160;want&#160;to&#160;add&#160;a&#160;pipeline&#160;to&#160;nf-core,&#160;please&#160;</text><text class="terminal-1144763792-r15" x="707.6" y="483.6" textLength="158.6" clip-path="url(#terminal-1144763792-line-19)">join&#160;on&#160;Slack</text><text class="terminal-1144763792-r14" x="866.2" y="483.6" textLength="292.8" clip-path="url(#terminal-1144763792-line-19)">&#160;and&#160;discuss&#160;your&#160;plans&#160;</text><text class="terminal-1144763792-r1" x="1220" y="483.6" textLength="12.2" clip-path="url(#terminal-1144763792-line-19)">
+  </text><text class="terminal-1144763792-r13" x="48.8" y="508" textLength="12.2" clip-path="url(#terminal-1144763792-line-20)">▌</text><text class="terminal-1144763792-r14" x="73.2" y="508" textLength="500.2" clip-path="url(#terminal-1144763792-line-20)">with&#160;the&#160;community&#160;as&#160;early&#160;as&#160;possible;&#160;</text><text class="terminal-1144763792-r16" x="573.4" y="508" textLength="512.4" clip-path="url(#terminal-1144763792-line-20)">ideally&#160;before&#160;you&#160;start&#160;on&#160;your&#160;pipeline!</text><text class="terminal-1144763792-r14" x="1085.8" y="508" textLength="61" clip-path="url(#terminal-1144763792-line-20)">&#160;See&#160;</text><text class="terminal-1144763792-r1" x="1220" y="508" textLength="12.2" clip-path="url(#terminal-1144763792-line-20)">
+  </text><text class="terminal-1144763792-r13" x="48.8" y="532.4" textLength="12.2" clip-path="url(#terminal-1144763792-line-21)">▌</text><text class="terminal-1144763792-r14" x="73.2" y="532.4" textLength="48.8" clip-path="url(#terminal-1144763792-line-21)">the&#160;</text><text class="terminal-1144763792-r15" x="122" y="532.4" textLength="219.6" clip-path="url(#terminal-1144763792-line-21)">nf-core&#160;guidelines</text><text class="terminal-1144763792-r14" x="341.6" y="532.4" textLength="109.8" clip-path="url(#terminal-1144763792-line-21)">&#160;and&#160;the&#160;</text><text class="terminal-1144763792-r15" x="451.4" y="532.4" textLength="170.8" clip-path="url(#terminal-1144763792-line-21)">#new-pipelines</text><text class="terminal-1144763792-r14" x="622.2" y="532.4" textLength="439.2" clip-path="url(#terminal-1144763792-line-21)">&#160;Slack&#160;channel&#160;for&#160;more&#160;information.</text><text class="terminal-1144763792-r1" x="1220" y="532.4" textLength="12.2" clip-path="url(#terminal-1144763792-line-21)">
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+  </text><text class="terminal-1144763792-r18" x="500.2" y="630" textLength="109.8" clip-path="url(#terminal-1144763792-line-25)">Let&#x27;s&#160;go!</text><text class="terminal-1144763792-r1" x="1220" y="630" textLength="12.2" clip-path="url(#terminal-1144763792-line-25)">
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+  </text><text class="terminal-1144763792-r11" x="0" y="1215.6" textLength="36.6" clip-path="url(#terminal-1144763792-line-49)">&#160;D&#160;</text><text class="terminal-1144763792-r20" x="36.6" y="1215.6" textLength="219.6" clip-path="url(#terminal-1144763792-line-49)">&#160;Toggle&#160;dark&#160;mode&#160;</text><text class="terminal-1144763792-r11" x="256.2" y="1215.6" textLength="36.6" clip-path="url(#terminal-1144763792-line-49)">&#160;Q&#160;</text><text class="terminal-1144763792-r20" x="292.8" y="1215.6" textLength="73.2" clip-path="url(#terminal-1144763792-line-49)">&#160;Quit&#160;</text>
+      </g>
+      </g>
+  </svg>
+  
+  '''
+# ---
diff --git a/tests/data/pipeline_create_template.yml b/tests/data/pipeline_create_template.yml
index 12e48e9c27..0ed534aa10 100644
--- a/tests/data/pipeline_create_template.yml
+++ b/tests/data/pipeline_create_template.yml
@@ -1 +1,6 @@
-prefix: testprefix
+name: test
+description: just for 4w3s0m3 tests
+author: Chuck Norris
+version: 1.0.0
+force: True
+org: testprefix
diff --git a/tests/data/pipeline_create_template_skip.yml b/tests/data/pipeline_create_template_skip.yml
index b69175e0bb..ed498cb732 100644
--- a/tests/data/pipeline_create_template_skip.yml
+++ b/tests/data/pipeline_create_template_skip.yml
@@ -1,5 +1,11 @@
-prefix: testprefix
-skip:
+name: test
+description: just for 4w3s0m3 tests
+author: Chuck Norris
+version: 1.0.0
+force: True
+org: testprefix
+is_nfcore: False
+skip_features:
   - github
   - ci
   - github_badges
diff --git a/tests/lint/configs.py b/tests/lint/configs.py
index b50a1393aa..8610910cd8 100644
--- a/tests/lint/configs.py
+++ b/tests/lint/configs.py
@@ -2,8 +2,8 @@
 
 import yaml
 
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create
 
 
 def test_withname_in_modules_config(self):
diff --git a/tests/lint/nextflow_config.py b/tests/lint/nextflow_config.py
index 06af8c4fb8..4bd7959448 100644
--- a/tests/lint/nextflow_config.py
+++ b/tests/lint/nextflow_config.py
@@ -2,8 +2,8 @@
 import re
 from pathlib import Path
 
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create.create
 
 
 def test_nextflow_config_example_pass(self):
diff --git a/tests/lint/nfcore_yml.py b/tests/lint/nfcore_yml.py
index 474ccd48fc..9d745a6346 100644
--- a/tests/lint/nfcore_yml.py
+++ b/tests/lint/nfcore_yml.py
@@ -1,8 +1,8 @@
 import re
 from pathlib import Path
 
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create
 
 
 def test_nfcore_yml_pass(self):
diff --git a/tests/lint/template_strings.py b/tests/lint/template_strings.py
index ac0ae01681..50c956b217 100644
--- a/tests/lint/template_strings.py
+++ b/tests/lint/template_strings.py
@@ -1,8 +1,8 @@
 import subprocess
 from pathlib import Path
 
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create
 
 
 def test_template_strings(self):
@@ -16,7 +16,6 @@ def test_template_strings(self):
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
     result = lint_obj.template_strings()
-    print(result["failed"])
     assert len(result["failed"]) == 1
     assert len(result["ignored"]) == 0
 
diff --git a/tests/lint/version_consistency.py b/tests/lint/version_consistency.py
index c682800646..4763020fb9 100644
--- a/tests/lint/version_consistency.py
+++ b/tests/lint/version_consistency.py
@@ -1,5 +1,5 @@
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create.create
 
 
 def test_version_consistency(self):
@@ -11,4 +11,4 @@ def test_version_consistency(self):
 
     result = lint_obj.version_consistency()
     assert result["passed"] == ["Version tags are numeric and consistent between container, release tag and config."]
-    assert result["failed"] == ["manifest.version was not numeric: 1.0dev!"]
+    assert result["failed"] == ["manifest.version was not numeric: 1.0.0dev!"]
diff --git a/tests/modules/patch.py b/tests/modules/patch.py
index dc939c7ea7..513ea8a433 100644
--- a/tests/modules/patch.py
+++ b/tests/modules/patch.py
@@ -349,7 +349,7 @@ def test_remove_patch(self):
         "modules", REPO_NAME, BISMARK_ALIGN, patch_fn
     )
 
-    with mock.patch.object(nf_core.create.questionary, "confirm") as mock_questionary:
+    with mock.patch.object(nf_core.components.patch.questionary, "confirm") as mock_questionary:
         mock_questionary.unsafe_ask.return_value = True
         patch_obj.remove(BISMARK_ALIGN)
     # Check that the diff file has been removed
diff --git a/tests/test_bump_version.py b/tests/test_bump_version.py
index c697d34287..059e18e92e 100644
--- a/tests/test_bump_version.py
+++ b/tests/test_bump_version.py
@@ -5,7 +5,7 @@
 import yaml
 
 import nf_core.bump_version
-import nf_core.create
+import nf_core.pipelines.create.create
 import nf_core.utils
 
 
@@ -16,8 +16,8 @@ def test_bump_pipeline_version(datafiles, tmp_path):
 
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
+    create_obj = nf_core.pipelines.create.create.PipelineCreate(
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
@@ -36,8 +36,8 @@ def test_dev_bump_pipeline_version(datafiles, tmp_path):
     """Test that making a release works with a dev name and a leading v"""
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
+    create_obj = nf_core.pipelines.create.create.PipelineCreate(
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
@@ -55,8 +55,8 @@ def test_dev_bump_pipeline_version(datafiles, tmp_path):
 def test_bump_nextflow_version(datafiles, tmp_path):
     # Get a workflow and configs
     test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-    create_obj = nf_core.create.PipelineCreate(
-        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir, plain=True
+    create_obj = nf_core.pipelines.create.create.PipelineCreate(
+        "testpipeline", "This is a test pipeline", "Test McTestFace", no_git=True, outdir=test_pipeline_dir
     )
     create_obj.init_pipeline()
     pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 5df0a32418..76d167101a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -231,21 +231,17 @@ def test_licences_log_error(self, mock_lic):
         assert error_txt in captured_logs.output[-1]
         assert captured_logs.records[-1].levelname == "ERROR"
 
-    @mock.patch("nf_core.create.PipelineCreate")
+    @mock.patch("nf_core.pipelines.create.create.PipelineCreate")
     def test_create(self, mock_create):
         """Test nf-core pipeline is created and cli parameters are passed on."""
         params = {
-            "name": "pipeline name",
+            "name": "pipelinename",
             "description": "pipeline description",
             "author": "Kalle Anka",
-            "version": "1.2.3",
-            "force": None,
             "outdir": "/path/outdir",
-            "template-yaml": "file.yaml",
-            "plain": None,
         }
 
-        cmd = ["create"] + self.assemble_params(params)
+        cmd = ["pipelines", "create"] + self.assemble_params(params)
         result = self.invoke_cli(cmd)
 
         assert result.exit_code == 0
@@ -253,14 +249,39 @@ def test_create(self, mock_create):
             params["name"],
             params["description"],
             params["author"],
-            version=params["version"],
             force="force" in params,
+            version="1.0.0dev",
             outdir=params["outdir"],
-            template_yaml_path=params["template-yaml"],
-            plain="plain" in params,
+            template_config=None,
+            organisation="nf-core",
         )
         mock_create.return_value.init_pipeline.assert_called_once()
 
+    @mock.patch("nf_core.pipelines.create.create.PipelineCreate")
+    def test_create_error(self, mock_create):
+        """Test `nf-core pipelines create` run without providing all the arguments thorws an error."""
+        params = {
+            "name": "pipelinename",
+        }
+
+        cmd = ["pipelines", "create"] + self.assemble_params(params)
+        result = self.invoke_cli(cmd)
+
+        assert result.exit_code == 1
+        assert "Partial arguments supplied." in result.output
+
+    @mock.patch("nf_core.pipelines.create.PipelineCreateApp")
+    def test_create_app(self, mock_create):
+        """Test `nf-core pipelines create` runs an App."""
+        cmd = ["pipelines", "create"]
+        result = self.invoke_cli(cmd)
+
+        assert result.return_value == (0 or None)
+        assert "Launching interactive nf-core pipeline creation tool." in result.output
+
+        mock_create.assert_called_once_with()
+        mock_create.return_value.run.assert_called_once()
+
     @mock.patch("nf_core.utils.is_pipeline_directory")
     @mock.patch("nf_core.lint.run_linting")
     def test_lint(self, mock_lint, mock_is_pipeline):
diff --git a/tests/test_create.py b/tests/test_create.py
index e2672499cd..313b6f5354 100644
--- a/tests/test_create.py
+++ b/tests/test_create.py
@@ -3,12 +3,11 @@
 import os
 import unittest
 from pathlib import Path
-from unittest import mock
 
 import git
 import yaml
 
-import nf_core.create
+import nf_core.pipelines.create.create
 
 from .utils import with_temporary_folder
 
@@ -26,25 +25,24 @@ def setUp(self):
         self.default_branch = "default"
 
     def test_pipeline_creation(self):
-        pipeline = nf_core.create.PipelineCreate(
+        pipeline = nf_core.pipelines.create.create.PipelineCreate(
             name=self.pipeline_name,
             description=self.pipeline_description,
             author=self.pipeline_author,
             version=self.pipeline_version,
             no_git=False,
             force=True,
-            plain=True,
             default_branch=self.default_branch,
         )
 
-        assert pipeline.template_params["name"] == self.pipeline_name
-        assert pipeline.template_params["description"] == self.pipeline_description
-        assert pipeline.template_params["author"] == self.pipeline_author
-        assert pipeline.template_params["version"] == self.pipeline_version
+        assert pipeline.config.name == self.pipeline_name
+        assert pipeline.config.description == self.pipeline_description
+        assert pipeline.config.author == self.pipeline_author
+        assert pipeline.config.version == self.pipeline_version
 
     @with_temporary_folder
     def test_pipeline_creation_initiation(self, tmp_path):
-        pipeline = nf_core.create.PipelineCreate(
+        pipeline = nf_core.pipelines.create.create.PipelineCreate(
             name=self.pipeline_name,
             description=self.pipeline_description,
             author=self.pipeline_author,
@@ -52,7 +50,6 @@ def test_pipeline_creation_initiation(self, tmp_path):
             no_git=False,
             force=True,
             outdir=tmp_path,
-            plain=True,
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
@@ -60,20 +57,14 @@ def test_pipeline_creation_initiation(self, tmp_path):
         assert f" {self.default_branch}\n" in git.Repo.init(pipeline.outdir).git.branch()
         assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
         with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
-            assert "template" not in fh.read()
+            assert "template" in fh.read()
 
     @with_temporary_folder
     def test_pipeline_creation_initiation_with_yml(self, tmp_path):
-        pipeline = nf_core.create.PipelineCreate(
-            name=self.pipeline_name,
-            description=self.pipeline_description,
-            author=self.pipeline_author,
-            version=self.pipeline_version,
+        pipeline = nf_core.pipelines.create.create.PipelineCreate(
             no_git=False,
-            force=True,
             outdir=tmp_path,
-            template_yaml_path=PIPELINE_TEMPLATE_YML,
-            plain=True,
+            template_config=PIPELINE_TEMPLATE_YML,
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
@@ -86,23 +77,12 @@ def test_pipeline_creation_initiation_with_yml(self, tmp_path):
         with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
-            assert nfcore_yml["template"] == yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text())
+            assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
-    @mock.patch.object(nf_core.create.PipelineCreate, "customize_template")
-    @mock.patch.object(nf_core.create.questionary, "confirm")
     @with_temporary_folder
-    def test_pipeline_creation_initiation_customize_template(self, mock_questionary, mock_customize, tmp_path):
-        mock_questionary.unsafe_ask.return_value = True
-        mock_customize.return_value = {"prefix": "testprefix"}
-        pipeline = nf_core.create.PipelineCreate(
-            name=self.pipeline_name,
-            description=self.pipeline_description,
-            author=self.pipeline_author,
-            version=self.pipeline_version,
-            no_git=False,
-            force=True,
-            outdir=tmp_path,
-            default_branch=self.default_branch,
+    def test_pipeline_creation_initiation_customize_template(self, tmp_path):
+        pipeline = nf_core.pipelines.create.create.PipelineCreate(
+            outdir=tmp_path, template_config=PIPELINE_TEMPLATE_YML, default_branch=self.default_branch
         )
         pipeline.init_pipeline()
         assert os.path.isdir(os.path.join(pipeline.outdir, ".git"))
@@ -114,24 +94,16 @@ def test_pipeline_creation_initiation_customize_template(self, mock_questionary,
         with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
-            assert nfcore_yml["template"] == yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text())
+            assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
     @with_temporary_folder
     def test_pipeline_creation_with_yml_skip(self, tmp_path):
-        pipeline = nf_core.create.PipelineCreate(
-            name=self.pipeline_name,
-            description=self.pipeline_description,
-            author=self.pipeline_author,
-            version=self.pipeline_version,
-            no_git=False,
-            force=True,
+        pipeline = nf_core.pipelines.create.create.PipelineCreate(
             outdir=tmp_path,
-            template_yaml_path=PIPELINE_TEMPLATE_YML_SKIP,
-            plain=True,
+            template_config=PIPELINE_TEMPLATE_YML_SKIP,
             default_branch=self.default_branch,
         )
         pipeline.init_pipeline()
-        assert not os.path.isdir(os.path.join(pipeline.outdir, ".git"))
 
         # Check pipeline template yml has been dumped to `.nf-core.yml` and matches input
         assert not os.path.exists(os.path.join(pipeline.outdir, "pipeline_template.yml"))
@@ -139,7 +111,7 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
         with open(os.path.join(pipeline.outdir, ".nf-core.yml")) as fh:
             nfcore_yml = yaml.safe_load(fh)
             assert "template" in nfcore_yml
-            assert nfcore_yml["template"] == yaml.safe_load(PIPELINE_TEMPLATE_YML_SKIP.read_text())
+            assert yaml.safe_load(PIPELINE_TEMPLATE_YML.read_text()).items() <= nfcore_yml["template"].items()
 
         # Check that some of the skipped files are not present
         assert not os.path.exists(os.path.join(pipeline.outdir, "CODE_OF_CONDUCT.md"))
diff --git a/tests/test_create_app.py b/tests/test_create_app.py
new file mode 100644
index 0000000000..f01ea5b6bd
--- /dev/null
+++ b/tests/test_create_app.py
@@ -0,0 +1,291 @@
+"""Test Pipeline Create App"""
+
+from nf_core.pipelines.create import PipelineCreateApp
+
+
+async def test_app_bindings():
+    """Test that the app bindings work."""
+    app = PipelineCreateApp()
+    async with app.run_test() as pilot:
+        # Test pressing the D key
+        assert app.dark
+        await pilot.press("d")
+        assert not app.dark
+        await pilot.press("d")
+        assert app.dark
+
+        # Test pressing the Q key
+        await pilot.press("q")
+        assert app.return_code == 0
+
+
+def test_welcome(snap_compare):
+    """Test snapshot for the first screen in the app. The welcome screen."""
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50))
+
+
+def test_choose_type(snap_compare):
+    """Test snapshot for the choose_type screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_basic_details_nfcore(snap_compare):
+    """Test snapshot for the basic_details screen of an nf-core pipeline.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_basic_details_custom(snap_compare):
+    """Test snapshot for the basic_details screen of a custom pipeline.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press custom >
+        screen basic_details
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_custom")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_type_nfcore(snap_compare):
+    """Test snapshot for the type_nfcore screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_nfcore
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#name")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_type_nfcore_validation(snap_compare):
+    """Test snapshot for the type_nfcore screen.
+    Validation errors should appear when input fields are empty.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > press next >
+        ERRORS
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#next")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_type_custom(snap_compare):
+    """Test snapshot for the type_custom screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press custom >
+        screen basic_details > enter pipeline details > press next >
+        screen type_custom
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_custom")
+        await pilot.click("#name")
+        await pilot.press("tab")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_final_details(snap_compare):
+    """Test snapshot for the final_details screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_nfcore > press continue >
+        screen final_details
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#name")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+        await pilot.click("#continue")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_customisation_help(snap_compare):
+    """Test snapshot for the type_custom screen - showing help messages.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_custom > press Show more
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_custom")
+        await pilot.click("#name")
+        await pilot.press("tab")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+        await pilot.click("#igenomes")
+        await pilot.press("tab")
+        await pilot.press("enter")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_github_question(tmpdir, snap_compare):
+    """Test snapshot for the github_repo_question screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_nfcore > press continue >
+        screen final_details > press finish > close logging screen >
+        screen github_repo_question
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#name")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+        await pilot.click("#continue")
+        await pilot.press("backspace")
+        await pilot.press("tab")
+        await pilot.press(*str(tmpdir))
+        await pilot.click("#finish")
+        await pilot.app.workers.wait_for_complete()
+        await pilot.click("#close_screen")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_github_details(tmpdir, snap_compare):
+    """Test snapshot for the github_repo screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_nfcore > press continue >
+        screen final_details > press finish > close logging screen >
+        screen github_repo_question > press create repo >
+        screen github_repo
+    """
+
+    async def run_before(pilot) -> None:
+        delete = ["backspace"] * 50
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#name")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+        await pilot.click("#continue")
+        await pilot.press("backspace")
+        await pilot.press("tab")
+        await pilot.press(*str(tmpdir))
+        await pilot.click("#finish")
+        await pilot.app.workers.wait_for_complete()
+        await pilot.click("#close_screen")
+        await pilot.click("#github_repo")
+        await pilot.click("#gh_username")
+        await pilot.press(*delete)  # delete field automatically filled using github CLI
+        await pilot.press("tab")
+        await pilot.press(*delete)
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
+
+
+def test_github_exit_message(tmpdir, snap_compare):
+    """Test snapshot for the github_exit screen.
+    Steps to get to this screen:
+        screen welcome > press start >
+        screen choose_type > press nf-core >
+        screen basic_details > enter pipeline details > press next >
+        screen type_nfcore > press continue >
+        screen final_details > press finish > close logging screen >
+        screen github_repo_question > press create repo >
+        screen github_repo > press exit (close without creating a repo) >
+        screen github_exit
+    """
+
+    async def run_before(pilot) -> None:
+        await pilot.click("#start")
+        await pilot.click("#type_nfcore")
+        await pilot.click("#name")
+        await pilot.press("m", "y", "p", "i", "p", "e", "l", "i", "n", "e")
+        await pilot.press("tab")
+        await pilot.press("A", " ", "c", "o", "o", "l", " ", "d", "e", "s", "c", "r", "i", "p", "t", "i", "o", "n")
+        await pilot.press("tab")
+        await pilot.press("M", "e")
+        await pilot.click("#next")
+        await pilot.click("#continue")
+        await pilot.press("backspace")
+        await pilot.press("tab")
+        await pilot.press(*str(tmpdir))
+        await pilot.click("#finish")
+        await pilot.app.workers.wait_for_complete()
+        await pilot.click("#close_screen")
+        await pilot.click("#github_repo")
+        await pilot.click("#exit")
+
+    assert snap_compare("../nf_core/pipelines/create/__init__.py", terminal_size=(100, 50), run_before=run_before)
diff --git a/tests/test_download.py b/tests/test_download.py
index 3e0f11d579..e090885bb4 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -12,7 +12,7 @@
 
 import pytest
 
-import nf_core.create
+import nf_core.pipelines.create.create
 import nf_core.utils
 from nf_core.download import ContainerError, DownloadWorkflow, WorkflowRepo
 from nf_core.synced_repo import SyncedRepo
@@ -128,13 +128,12 @@ def test_download_configs(self, outdir):
     def test_wf_use_local_configs(self, tmp_path):
         # Get a workflow and configs
         test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
-        create_obj = nf_core.create.PipelineCreate(
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testpipeline",
             "This is a test pipeline",
             "Test McTestFace",
             no_git=True,
             outdir=test_pipeline_dir,
-            plain=True,
         )
         create_obj.init_pipeline()
 
diff --git a/tests/test_launch.py b/tests/test_launch.py
index 79dbe3fb97..043055a2d5 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -8,8 +8,8 @@
 
 import pytest
 
-import nf_core.create
 import nf_core.launch
+import nf_core.pipelines.create.create
 
 from .utils import create_tmp_pipeline, with_temporary_file, with_temporary_folder
 
@@ -65,8 +65,8 @@ def test_get_pipeline_schema(self):
     def test_make_pipeline_schema(self, tmp_path):
         """Create a workflow, but delete the schema file, then try to load it"""
         test_pipeline_dir = os.path.join(tmp_path, "wf")
-        create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "", "", outdir=test_pipeline_dir, no_git=True, plain=True
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            "testpipeline", "a description", "Me", outdir=test_pipeline_dir, no_git=True
         )
         create_obj.init_pipeline()
         os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json"))
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 15c1550e72..aaf8330800 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -9,8 +9,8 @@
 
 import yaml
 
-import nf_core.create
 import nf_core.lint
+import nf_core.pipelines.create.create
 
 from .utils import with_temporary_folder
 
@@ -21,13 +21,13 @@ class TestLint(unittest.TestCase):
     def setUp(self):
         """Function that runs at start of tests for common resources
 
-        Use nf_core.create() to make a pipeline that we can use for testing
+        Use nf_core.pipelines.create() to make a pipeline that we can use for testing
         """
 
         self.tmp_dir = tempfile.mkdtemp()
         self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline")
-        self.create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir, plain=True
+        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            "testpipeline", "This is a test pipeline", "Test McTestFace", outdir=self.test_pipeline_dir
         )
         self.create_obj.init_pipeline()
 
diff --git a/tests/test_modules.py b/tests/test_modules.py
index d3d99abadd..a122f16b69 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -10,8 +10,8 @@
 import responses
 import yaml
 
-import nf_core.create
 import nf_core.modules
+import nf_core.pipelines.create.create
 
 from .utils import (
     GITLAB_BRANCH_TEST_BRANCH,
@@ -99,6 +99,7 @@ def setUp(self):
 
         # Set up the schema
         self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
+
         # Set up install objects
         self.mods_install = nf_core.modules.ModuleInstall(self.pipeline_dir, prompt=False, force=True)
         self.mods_install_old = nf_core.modules.ModuleInstall(
diff --git a/tests/test_params_file.py b/tests/test_params_file.py
index 13c82f5188..673139c3b2 100644
--- a/tests/test_params_file.py
+++ b/tests/test_params_file.py
@@ -4,7 +4,7 @@
 import tempfile
 from pathlib import Path
 
-import nf_core.create
+import nf_core.pipelines.create.create
 import nf_core.schema
 from nf_core.params_file import ParamsFileBuilder
 
@@ -21,8 +21,8 @@ def setup_class(cls):
         # Create a test pipeline in temp directory
         cls.tmp_dir = tempfile.mkdtemp()
         cls.template_dir = os.path.join(cls.tmp_dir, "wf")
-        create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "", "", outdir=cls.template_dir, no_git=True, plain=True
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            "testpipeline", "a description", "Me", outdir=cls.template_dir, no_git=True
         )
         create_obj.init_pipeline()
 
diff --git a/tests/test_schema.py b/tests/test_schema.py
index e0921908d4..b4be7ae455 100644
--- a/tests/test_schema.py
+++ b/tests/test_schema.py
@@ -12,7 +12,7 @@
 import requests
 import yaml
 
-import nf_core.create
+import nf_core.pipelines.create.create
 import nf_core.schema
 
 from .utils import with_temporary_file, with_temporary_folder
@@ -29,8 +29,8 @@ def setUp(self):
         # Create a test pipeline in temp directory
         self.tmp_dir = tempfile.mkdtemp()
         self.template_dir = os.path.join(self.tmp_dir, "wf")
-        create_obj = nf_core.create.PipelineCreate(
-            "testpipeline", "", "", outdir=self.template_dir, no_git=True, plain=True
+        create_obj = nf_core.pipelines.create.create.PipelineCreate(
+            "testpipeline", "a description", "Me", outdir=self.template_dir, no_git=True
         )
         create_obj.init_pipeline()
 
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 0a9224002a..59de1967e4 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -6,8 +6,8 @@
 import unittest
 from pathlib import Path
 
-import nf_core.create
 import nf_core.modules
+import nf_core.pipelines.create.create
 import nf_core.subworkflows
 
 from .utils import (
@@ -63,6 +63,7 @@ def setUp(self):
 
         # Set up the pipeline structure
         self.tmp_dir, self.template_dir, self.pipeline_name, self.pipeline_dir = create_tmp_pipeline()
+
         # Set up the nf-core/modules repo dummy
         self.nfcore_modules = create_modules_repo_dummy(self.tmp_dir)
 
diff --git a/tests/test_sync.py b/tests/test_sync.py
index b94968cd4c..40e68dc7dc 100644
--- a/tests/test_sync.py
+++ b/tests/test_sync.py
@@ -11,7 +11,7 @@
 import git
 import pytest
 
-import nf_core.create
+import nf_core.pipelines.create.create
 import nf_core.sync
 
 from .utils import with_temporary_folder
@@ -25,12 +25,11 @@ def setUp(self):
         self.tmp_dir = tempfile.mkdtemp()
         self.pipeline_dir = os.path.join(self.tmp_dir, "testpipeline")
         default_branch = "master"
-        self.create_obj = nf_core.create.PipelineCreate(
+        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testing",
             "test pipeline",
             "tester",
             outdir=self.pipeline_dir,
-            plain=True,
             default_branch=default_branch,
         )
         self.create_obj.init_pipeline()
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 145060450f..85f4e3c548 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -10,8 +10,8 @@
 import pytest
 import requests
 
-import nf_core.create
 import nf_core.list
+import nf_core.pipelines.create.create
 import nf_core.utils
 
 from .utils import with_temporary_folder
@@ -34,17 +34,16 @@ class TestUtils(unittest.TestCase):
     def setUp(self):
         """Function that runs at start of tests for common resources
 
-        Use nf_core.create() to make a pipeline that we can use for testing
+        Use nf_core.pipelines.create() to make a pipeline that we can use for testing
         """
         self.tmp_dir = tempfile.mkdtemp()
         self.test_pipeline_dir = os.path.join(self.tmp_dir, "nf-core-testpipeline")
-        self.create_obj = nf_core.create.PipelineCreate(
+        self.create_obj = nf_core.pipelines.create.create.PipelineCreate(
             "testpipeline",
             "This is a test pipeline",
             "Test McTestFace",
             no_git=True,
             outdir=self.test_pipeline_dir,
-            plain=True,
         )
         self.create_obj.init_pipeline()
         # Base Pipeline object on this directory
diff --git a/tests/utils.py b/tests/utils.py
index 89c1328818..9a0fd0896f 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -9,8 +9,8 @@
 
 import responses
 
-import nf_core.create
 import nf_core.modules
+import nf_core.pipelines.create.create
 
 OLD_TRIMGALORE_SHA = "9b7a3bdefeaad5d42324aa7dd50f87bea1b04386"
 OLD_TRIMGALORE_BRANCH = "mimic-old-trimgalore"
@@ -102,8 +102,8 @@ def create_tmp_pipeline() -> Tuple[str, str, str, str]:
     pipeline_name = "mypipeline"
     pipeline_dir = os.path.join(tmp_dir, pipeline_name)
 
-    nf_core.create.PipelineCreate(
-        pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir, plain=True
+    nf_core.pipelines.create.create.PipelineCreate(
+        pipeline_name, "it is mine", "me", no_git=True, outdir=pipeline_dir
     ).init_pipeline()
 
     # return values to instance variables for later use in test methods