diff --git a/.gitignore b/.gitignore
index 34cd784c6ee1..f12725dee401 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ test_output/
 tests/data/
 work/
 .github/CODEOWNERS-tmp
+conda_envs/
diff --git a/get_conda_envs.py b/get_conda_envs.py
new file mode 100644
index 000000000000..1f68edebb87d
--- /dev/null
+++ b/get_conda_envs.py
@@ -0,0 +1,78 @@
+import hashlib
+import os
+from pathlib import Path
+
+import yaml
+from rich.console import Console
+from rich.panel import Panel
+from rich.progress import BarColumn, Progress, SpinnerColumn, TextColumn
+
+console = Console()
+
+
+def find_and_normalize_yaml():
+    base_dir = Path("modules/nf-core")
+    output_dir = Path("conda_envs")
+    output_dir.mkdir(exist_ok=True)
+
+    processed_hashes = set()
+    total_files = 0
+    written_files = 0
+    skipped_files = 0
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[progress.description]{task.description}"),
+        BarColumn(),
+        TextColumn("[progress.percentage]{task.percentage:>3.0f}%"),
+        console=console,
+    ) as progress:
+        task = progress.add_task("[green]Processing files...", total=None)
+
+        for root, dirs, files in os.walk(base_dir):
+            for file in files:
+                if file == "environment.yml":
+                    total_files += 1
+                    file_path = Path(root) / file
+                    was_written = normalize_and_save_yaml(file_path, output_dir, processed_hashes, progress, task)
+                    if was_written:
+                        written_files += 1
+                    else:
+                        skipped_files += 1
+
+    console.print(
+        Panel.fit(
+            f"[bold green]✨ Summary ✨[/]\n\n"
+            f"📁 Total environment.yml files found: [cyan]{total_files}[/]\n"
+            f"📝 Unique files written: [cyan]{written_files}[/]\n"
+            f"🔄 Duplicate files skipped: [cyan]{skipped_files}[/]",
+            title="Conda Environment Processing Results",
+            border_style="bold blue",
+        )
+    )
+
+
+def normalize_and_save_yaml(file_path, output_dir, processed_hashes, progress, task):
+    with open(file_path) as f:
+        data = yaml.safe_load(f)
+
+    normalized_yaml = yaml.dump(data, sort_keys=False)
+    yaml_hash = hashlib.md5(normalized_yaml.encode()).hexdigest()
+
+    if yaml_hash not in processed_hashes:
+        output_file = output_dir / f"{yaml_hash}.yml"
+        with open(output_file, "w") as f:
+            f.write(normalized_yaml)
+        processed_hashes.add(yaml_hash)
+        progress.console.print(f"[green]✅   Saved:[/] {file_path} [dim](location: {output_file})[/]")
+        return True
+    else:
+        progress.console.print(f"[yellow]⏭️ Skipped:[/] {file_path}")
+        return False
+
+    progress.update(task, advance=1)
+
+
+if __name__ == "__main__":
+    console.print("[bold magenta]Starting Conda Environment Processing...[/]\n")
+    find_and_normalize_yaml()
diff --git a/get_wave_images.py b/get_wave_images.py
new file mode 100644
index 000000000000..548a2a5ffdb3
--- /dev/null
+++ b/get_wave_images.py
@@ -0,0 +1,115 @@
+import logging
+import subprocess
+from pathlib import Path
+
+import yaml
+from rich.console import Console
+from rich.logging import RichHandler
+
+# Configure rich console
+console = Console()
+
+# Configure logging with rich
+logging.basicConfig(
+    level="DEBUG",  # Set to DEBUG to capture all messages
+    format="%(message)s",
+    datefmt="[%X]",
+    handlers=[
+        RichHandler(console=console, rich_tracebacks=True, show_time=False, level="INFO"),
+    ],
+)
+logger = logging.getLogger("rich")
+
+
+def get_wave_image(env_file):
+    logger.debug(f"Requesting Wave image for {env_file}")
+    try:
+        result = subprocess.run(
+            ["wave", "--conda-file", env_file, "--await"], capture_output=True, text=True, check=True
+        )
+        logger.debug(f"Successfully obtained Wave image for {env_file}")
+        return result.stdout.strip()
+    except subprocess.CalledProcessError as e:
+        logger.error(f"Error running Wave CLI for {env_file}: {e}")
+        return None
+
+
+def update_meta_yml(meta_file, docker_image):
+    logger.debug(f"Updating {meta_file} with Docker image")
+
+    # Read the existing content
+    with open(meta_file) as f:
+        content = f.read()
+        meta_data = yaml.safe_load(content) or {}
+
+    # Check if 'containers' key exists
+    if "containers" not in meta_data:
+        # If not, add it with proper indentation
+        content += f"\ncontainers:\n  docker_x86: {docker_image}\n"
+    else:
+        # If it exists, add docker_x86 under it
+        lines = content.splitlines()
+        containers_index = next(i for i, line in enumerate(lines) if line.strip() == "containers:")
+        indent = len(lines[containers_index + 1]) - len(lines[containers_index + 1].lstrip())
+        lines.insert(containers_index + 1, " " * indent + f"docker_x86: {docker_image}")
+        content = "\n".join(lines) + "\n"
+
+    # Write the updated content back to the file
+    with open(meta_file, "w") as f:
+        f.write(content)
+
+    logger.debug(f"Successfully updated {meta_file}")
+
+
+def process_module_directory(directory, modname):
+    env_file = directory / "environment.yml"
+    meta_file = directory / "meta.yml"
+
+    if not env_file.exists():
+        logger.debug(f"Skipping {directory.name}: environment.yml not found")
+        return
+    if not meta_file.exists():
+        logger.debug(f"Skipping {directory.name}: meta.yml not found")
+        return
+
+    logger.debug(f"Checking {meta_file}")
+    with open(meta_file) as f:
+        meta_data = yaml.safe_load(f) or {}
+
+    if "containers" in meta_data and "docker_x86" in meta_data["containers"]:
+        logger.debug(f"Skipped {meta_file} (already contains docker_x86)")
+        return
+
+    logger.debug(f"docker_x86 not found in {meta_file}, proceeding with Wave CLI")
+    logger.info(f"Processing: {modname}")
+    docker_image = get_wave_image(str(env_file))
+    if docker_image:
+        update_meta_yml(meta_file, docker_image)
+        logger.debug(f"Got image: {docker_image}")
+    else:
+        logger.error(f"Failed to update {meta_file}: No Docker image obtained")
+
+
+def process_modules():
+    modules_dir = Path("modules/nf-core")
+    logger.debug(f"Processing modules in {modules_dir}")
+
+    for module_dir in modules_dir.iterdir():
+        if not module_dir.is_dir():
+            continue
+
+        # Check if the module directory itself contains environment.yml and meta.yml
+        if (module_dir / "environment.yml").exists() and (module_dir / "meta.yml").exists():
+            process_module_directory(module_dir, module_dir.name)
+        else:
+            # If not, check for subdirectories
+            for subdir in module_dir.iterdir():
+                if subdir.is_dir():
+                    logger.debug(f"Processing subdirectory: {subdir.name}")
+                    process_module_directory(subdir, f"{module_dir.name}/{subdir.name}")
+
+
+if __name__ == "__main__":
+    console.rule("[bold blue]Starting module processing[/bold blue]")
+    process_modules()
+    console.rule("[bold blue]Finished processing all modules[/bold blue]")
diff --git a/modules_cli.py b/modules_cli.py
new file mode 100644
index 000000000000..2aad1c9e5d66
--- /dev/null
+++ b/modules_cli.py
@@ -0,0 +1,288 @@
+import argparse
+import hashlib
+import logging
+import os
+import subprocess
+from pathlib import Path
+
+import yaml
+from rich.console import Console
+from rich.logging import RichHandler
+from rich.panel import Panel
+from rich.progress import BarColumn, Progress, SpinnerColumn, TextColumn
+
+
+console = Console()
+
+
+def configure_logging():
+    """Configure rich logging output."""
+    logging.basicConfig(
+        level="DEBUG",
+        format="%(message)s",
+        datefmt="[%X]",
+        handlers=[
+            RichHandler(
+                console=console,
+                rich_tracebacks=True,
+                show_time=False,
+                level="INFO",
+            ),
+        ],
+    )
+    return logging.getLogger("rich")
+
+
+logger = configure_logging()
+
+
+# ---------------------------------------------------------------------------
+# Conda environment collection (from get_conda_envs.py)
+# ---------------------------------------------------------------------------
+
+def find_and_normalize_yaml(module: str | None = None):
+    """
+    Find all environment.yml files under modules/nf-core (optionally limited to
+    a single module) and write de-duplicated, normalised copies to conda_envs/.
+
+    If `module` is provided, it should be a path relative to modules/nf-core,
+    e.g. "tcoffee/align".
+    """
+    base_dir = Path("modules/nf-core")
+    if module:
+        base_dir = base_dir / module
+
+    output_dir = Path("conda_envs")
+    output_dir.mkdir(exist_ok=True)
+
+    processed_hashes: set[str] = set()
+    total_files = 0
+    written_files = 0
+    skipped_files = 0
+
+    with Progress(
+        SpinnerColumn(),
+        TextColumn("[progress.description]{task.description}"),
+        BarColumn(),
+        TextColumn("[progress.percentage]{task.percentage:>3.0f}%"),
+        console=console,
+    ) as progress:
+        task = progress.add_task("[green]Processing files...", total=None)
+
+        for root, _, files in os.walk(base_dir):
+            for file in files:
+                if file == "environment.yml":
+                    total_files += 1
+                    file_path = Path(root) / file
+                    was_written = normalize_and_save_yaml(
+                        file_path, output_dir, processed_hashes
+                    )
+                    if was_written:
+                        written_files += 1
+                    else:
+                        skipped_files += 1
+
+                    progress.update(task, advance=1)
+
+    console.print(
+        Panel.fit(
+            f"[bold green]✨ Summary ✨[/]\n\n"
+            f"📁 Total environment.yml files found: [cyan]{total_files}[/]\n"
+            f"📝 Unique files written: [cyan]{written_files}[/]\n"
+            f"🔄 Duplicate files skipped: [cyan]{skipped_files}[/]",
+            title="Conda Environment Processing Results",
+            border_style="bold blue",
+        )
+    )
+
+
+def normalize_and_save_yaml(
+    file_path: Path, output_dir: Path, processed_hashes: set[str]
+) -> bool:
+    with open(file_path) as f:
+        data = yaml.safe_load(f)
+
+    normalized_yaml = yaml.dump(data, sort_keys=False)
+    yaml_hash = hashlib.md5(normalized_yaml.encode()).hexdigest()
+
+    if yaml_hash not in processed_hashes:
+        output_file = output_dir / f"{yaml_hash}.yml"
+        with open(output_file, "w") as f:
+            f.write(normalized_yaml)
+        processed_hashes.add(yaml_hash)
+        console.print(
+            f"[green]✅   Saved:[/] {file_path} [dim](location: {output_file})[/]"
+        )
+        return True
+
+    console.print(f"[yellow]⏭️ Skipped:[/] {file_path}")
+    return False
+
+
+# ---------------------------------------------------------------------------
+# Wave image generation and meta.yml update (from get_wave_images.py)
+# ---------------------------------------------------------------------------
+
+def get_wave_image(env_file: str) -> str | None:
+    logger.debug(f"Requesting Wave image for {env_file}")
+    try:
+        # Always use --freeze when generating images
+        result = subprocess.run(
+            ["wave", "--conda-file", env_file, "--await", "--freeze"],
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        logger.debug(f"Successfully obtained Wave image for {env_file}")
+        return result.stdout.strip()
+    except subprocess.CalledProcessError as e:
+        logger.error(f"Error running Wave CLI for {env_file}: {e}")
+        return None
+
+
+def update_meta_yml(meta_file: Path, docker_image: str) -> None:
+    logger.debug(f"Updating {meta_file} with Docker image")
+
+    # Read the existing content
+    with open(meta_file) as f:
+        content = f.read()
+        meta_data = yaml.safe_load(content) or {}
+
+    # Check if 'containers' key exists
+    if "containers" not in meta_data:
+        # If not, add it with proper indentation
+        content += f"\ncontainers:\n  docker_x86: {docker_image}\n"
+    else:
+        # If it exists, add docker_x86 under it
+        lines = content.splitlines()
+        containers_index = next(
+            i for i, line in enumerate(lines) if line.strip() == "containers:"
+        )
+        indent = len(lines[containers_index + 1]) - len(
+            lines[containers_index + 1].lstrip()
+        )
+        lines.insert(containers_index + 1, " " * indent + f"docker_x86: {docker_image}")
+        content = "\n".join(lines) + "\n"
+
+    # Write the updated content back to the file
+    with open(meta_file, "w") as f:
+        f.write(content)
+
+    logger.debug(f"Successfully updated {meta_file}")
+
+
+def process_module_directory(directory: Path, modname: str) -> None:
+    env_file = directory / "environment.yml"
+    meta_file = directory / "meta.yml"
+
+    if not env_file.exists():
+        logger.debug(f"Skipping {directory}: environment.yml not found")
+        return
+    if not meta_file.exists():
+        logger.debug(f"Skipping {directory}: meta.yml not found")
+        return
+
+    logger.debug(f"Checking {meta_file}")
+    with open(meta_file) as f:
+        meta_data = yaml.safe_load(f) or {}
+
+    if "containers" in meta_data and "docker_x86" in meta_data["containers"]:
+        logger.debug(f"Skipped {meta_file} (already contains docker_x86)")
+        return
+
+    logger.debug(f"docker_x86 not found in {meta_file}, proceeding with Wave CLI")
+    logger.info(f"Processing: {modname}")
+    docker_image = get_wave_image(str(env_file))
+    if docker_image:
+        update_meta_yml(meta_file, docker_image)
+        logger.debug(f"Got image: {docker_image}")
+    else:
+        logger.error(f"Failed to update {meta_file}: No Docker image obtained")
+
+
+def process_modules(module: str | None = None) -> None:
+    """
+    Walk modules/nf-core and populate docker_x86 using Wave images.
+
+    If `module` is provided, only that module (e.g. "tcoffee/align") is processed.
+    """
+    modules_dir = Path("modules/nf-core")
+    logger.debug(f"Processing modules in {modules_dir}")
+
+    # If a specific module path is requested, restrict traversal to that path
+    if module:
+        target = modules_dir / module
+        if not target.exists():
+            logger.error(f"Requested module '{module}' not found under {modules_dir}")
+            return
+
+        # If the target itself is a module directory with the files, process it
+        if (target / "environment.yml").exists() and (target / "meta.yml").exists():
+            process_module_directory(target, module)
+            return
+
+        # Otherwise, search its subdirectories
+        for subdir in target.iterdir():
+            if subdir.is_dir():
+                modname = f"{module}/{subdir.name}"
+                logger.debug(f"Processing subdirectory: {modname}")
+                process_module_directory(subdir, modname)
+        return
+
+    # No specific module requested: process all modules
+    for module_dir in modules_dir.iterdir():
+        if not module_dir.is_dir():
+            continue
+
+        # Check if the module directory itself contains environment.yml and meta.yml
+        if (module_dir / "environment.yml").exists() and (
+            module_dir / "meta.yml"
+        ).exists():
+            process_module_directory(module_dir, module_dir.name)
+        else:
+            # If not, check for subdirectories
+            for subdir in module_dir.iterdir():
+                if subdir.is_dir():
+                    modname = f"{module_dir.name}/{subdir.name}"
+                    logger.debug(f"Processing subdirectory: {modname}")
+                    process_module_directory(subdir, modname)
+
+
+# ---------------------------------------------------------------------------
+# CLI
+# ---------------------------------------------------------------------------
+
+
+def parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        description=(
+            "Collect unique Conda environments and generate Wave images to "
+            "populate docker_x86 entries in nf-core module meta.yml files."
+        )
+    )
+    parser.add_argument(
+        "-m",
+        "--module",
+        help=(
+            "Only process a single nf-core module, "
+            "e.g. 'tcoffee/align'. By default all modules are processed."
+        ),
+    )
+    return parser.parse_args()
+
+
+def main():
+    args = parse_args()
+
+    console.rule("[bold magenta]Starting Conda environment processing[/bold magenta]")
+    find_and_normalize_yaml(module=args.module)
+
+    console.rule("[bold blue]Starting Wave image generation[/bold blue]")
+    process_modules(module=args.module)
+    console.rule("[bold blue]Finished processing modules[/bold blue]")
+
+
+if __name__ == "__main__":
+    main()
+
+