diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 1bd2e27fb0..8fdd2bd7e1 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -33,7 +33,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 46152d92a7..654d248f79 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       # Get the repo code
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 8f3c5fdb47..7cff154a08 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - uses: actions/checkout@v3
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a909ccf07..65a967e9c6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,13 @@
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
 - Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
+- Updates seqeralabs/action-tower-launch to v2.0.0 ([#2301](https://github.com/nf-core/tools/pull/2301))
 - Remove schema validation from `lib` folder and use Nextflow [nf-validation plugin](https://nextflow-io.github.io/nf-validation/) instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Fix parsing of container directive when it is not typical nf-core format ([#2306](https://github.com/nf-core/tools/pull/2306))
+- Add ability to specify custom registry for linting modules, defaults to quay.io ([#2313](https://github.com/nf-core/tools/pull/2313))
+- Add `singularity.registry = 'quay.io'` in pipeline template
+- Bump minimum required NF version in pipeline template from `22.10.1` -> `23.04.0`
+- Add ability to interpret `docker.registry` from `nextflow.config` file. If not found defaults to quay.io. ([#2318](https://github.com/nf-core/tools/pull/2318))
 
 ### Download
 
diff --git a/README.md b/README.md
index dacb50ebc4..5d5791c109 100644
--- a/README.md
+++ b/README.md
@@ -941,6 +941,8 @@ before_command: sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/m
 
 To run unit tests of a module that you have installed or the test created by the command [`nf-core modules create-test-yml`](#create-a-module-test-config-file), you can use `nf-core modules test` command. This command runs the tests specified in `modules/tests/software/<tool>/<subtool>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new module to add the new files to your git index.
+
 You can specify the module name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX
@@ -1199,6 +1201,8 @@ extra_env:
 
 To run unit tests of a subworkflow that you have installed or the test created by the command [`nf-core subworkflow create-test-yml`](#create-a-subworkflow-test-config-file), you can use `nf-core subworkflows test` command. This command runs the tests specified in `tests/subworkflows/<subworkflow_name>/test.yml` file using [pytest](https://pytest-workflow.readthedocs.io/en/stable/).
 
+> This command uses the pytest argument `--git-aware` to avoid copying the whole `.git` directory and files ignored by `git`. This means that it will only include files listed by `git ls-files`. Remember to **commit your changes** after adding a new subworkflow to add the new files to your git index.
+
 You can specify the subworkflow name in the form TOOL/SUBTOOL in command line or provide it later by prompts.
 
 <!-- RICH-CODEX
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 6d6ded471a..ee5d675e0c 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -807,6 +807,14 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
+@click.option(
+    "-r",
+    "--registry",
+    type=str,
+    metavar="<registry>",
+    default=None,
+    help="Registry to use for containers. If not specified it will use docker.registry value in the nextflow.config file",
+)
 @click.option("-k", "--key", type=str, metavar="<test>", multiple=True, help="Run only these lint tests")
 @click.option("-a", "--all", is_flag=True, help="Run on all modules")
 @click.option("-w", "--fail-warned", is_flag=True, help="Convert warn tests to failures")
@@ -821,7 +829,7 @@ def create_test_yml(ctx, tool, run_tests, output, force, no_prompts):
 )
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
 def lint(
-    ctx, tool, dir, key, all, fail_warned, local, passed, sort_by, fix_version
+    ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version
 ):  # pylint: disable=redefined-outer-name
     """
     Lint one or more modules in a directory.
@@ -839,6 +847,7 @@ def lint(
         module_lint = ModuleLint(
             dir,
             fail_warned=fail_warned,
+            registry=ctx.params["registry"],
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             no_pull=ctx.obj["modules_repo_no_pull"],
@@ -846,6 +855,7 @@ def lint(
         )
         module_lint.lint(
             module=tool,
+            registry=registry,
             key=key,
             all_modules=all,
             print_results=True,
diff --git a/nf_core/components/components_test.py b/nf_core/components/components_test.py
index c2b9abf569..37e275aea8 100644
--- a/nf_core/components/components_test.py
+++ b/nf_core/components/components_test.py
@@ -7,6 +7,7 @@
 import pytest
 import questionary
 import rich
+from git import InvalidGitRepositoryError, Repo
 
 import nf_core.modules.modules_utils
 import nf_core.utils
@@ -179,6 +180,14 @@ def _run_pytests(self):
         console = rich.console.Console()
         console.rule(self.component_name, style="black")
 
+        # Check uncommitted changed
+        try:
+            repo = Repo(self.dir)
+            if repo.is_dirty():
+                log.warning("You have uncommitted changes. Make sure to commit last changes before running the tests.")
+        except InvalidGitRepositoryError:
+            pass
+
         # Set pytest arguments
         tag = self.component_name
         if self.component_type == "subworkflows":
diff --git a/nf_core/lint/readme.py b/nf_core/lint/readme.py
index ae5c542837..55060442b1 100644
--- a/nf_core/lint/readme.py
+++ b/nf_core/lint/readme.py
@@ -36,7 +36,7 @@ def readme(self):
 
     if "nextflow_badge" not in ignore_configs:
         # Check that there is a readme badge showing the minimum required version of Nextflow
-        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+        # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
         # and that it has the correct version
         nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
         match = re.search(nf_badge_re, content)
diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 24d673b1c2..9d8fb177cd 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -69,6 +69,7 @@ def __init__(
         remote_url=None,
         branch=None,
         no_pull=False,
+        registry=None,
         hide_progress=False,
     ):
         super().__init__(
@@ -114,6 +115,7 @@ def __init__(
                     )
                     for m in self.get_local_components()
                 ]
+            self.config = nf_core.utils.fetch_wf_config(self.dir, cache_config=True)
         else:
             module_dir = Path(self.dir, self.default_modules_path)
             self.all_remote_modules = [
@@ -124,6 +126,15 @@ def __init__(
             if not self.all_remote_modules:
                 raise LookupError("No modules in 'modules' directory")
 
+            # This could be better, perhaps glob for all nextflow.config files in?
+            self.config = nf_core.utils.fetch_wf_config(Path(self.dir).joinpath("tests", "config"), cache_config=True)
+
+        if registry is None:
+            self.registry = self.config.get("docker.registry", "quay.io")
+        else:
+            self.registry = registry
+        log.debug(f"Registry set to {self.registry}")
+
         self.lint_config = None
         self.modules_json = None
 
@@ -145,6 +156,7 @@ def get_all_lint_tests(is_pipeline):
     def lint(
         self,
         module=None,
+        registry="quay.io",
         key=(),
         all_modules=False,
         print_results=True,
@@ -227,11 +239,11 @@ def lint(
 
         # Lint local modules
         if local and len(local_modules) > 0:
-            self.lint_modules(local_modules, local=True, fix_version=fix_version)
+            self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
         if len(remote_modules) > 0:
-            self.lint_modules(remote_modules, local=False, fix_version=fix_version)
+            self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
 
         if print_results:
             self._print_results(show_passed=show_passed, sort_by=sort_by)
@@ -264,12 +276,13 @@ def filter_tests_by_key(self, key):
         # If -k supplied, only run these tests
         self.lint_tests = [k for k in self.lint_tests if k in key]
 
-    def lint_modules(self, modules, local=False, fix_version=False):
+    def lint_modules(self, modules, registry="quay.io", local=False, fix_version=False):
         """
         Lint a list of modules
 
         Args:
             modules ([NFCoreModule]): A list of module objects
+            registry (str): The container registry to use. Should be quay.io in most situations.
             local (boolean): Whether the list consist of local or nf-core modules
             fix_version (boolean): Fix the module version if a newer version is available
         """
@@ -290,9 +303,9 @@ def lint_modules(self, modules, local=False, fix_version=False):
 
             for mod in modules:
                 progress_bar.update(lint_progress, advance=1, test_name=mod.module_name)
-                self.lint_module(mod, progress_bar, local=local, fix_version=fix_version)
+                self.lint_module(mod, progress_bar, registry=registry, local=local, fix_version=fix_version)
 
-    def lint_module(self, mod, progress_bar, local=False, fix_version=False):
+    def lint_module(self, mod, progress_bar, registry, local=False, fix_version=False):
         """
         Perform linting on one module
 
@@ -311,7 +324,7 @@ def lint_module(self, mod, progress_bar, local=False, fix_version=False):
 
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, progress_bar)
+            self.main_nf(mod, fix_version, self.registry, progress_bar)
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:
@@ -323,7 +336,7 @@ def lint_module(self, mod, progress_bar, local=False, fix_version=False):
         else:
             for test_name in self.lint_tests:
                 if test_name == "main_nf":
-                    getattr(self, test_name)(mod, fix_version, progress_bar)
+                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
                 else:
                     getattr(self, test_name)(mod)
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 31b8adca3a..18d95bd37e 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -17,7 +17,7 @@
 log = logging.getLogger(__name__)
 
 
-def main_nf(module_lint_object, module, fix_version, progress_bar):
+def main_nf(module_lint_object, module, fix_version, registry, progress_bar):
     """
     Lint a ``main.nf`` module file
 
@@ -121,7 +121,7 @@ def main_nf(module_lint_object, module, fix_version, progress_bar):
         module.passed.append(("main_nf_script_outputs", "Process 'output' block found", module.main_nf))
 
     # Check the process definitions
-    if check_process_section(module, process_lines, fix_version, progress_bar):
+    if check_process_section(module, process_lines, registry, fix_version, progress_bar):
         module.passed.append(("main_nf_container", "Container versions match", module.main_nf))
     else:
         module.warned.append(("main_nf_container", "Container versions do not match", module.main_nf))
@@ -209,12 +209,20 @@ def check_when_section(self, lines):
     self.passed.append(("when_condition", "when: condition is unchanged", self.main_nf))
 
 
-def check_process_section(self, lines, fix_version, progress_bar):
-    """
-    Lint the section of a module between the process definition
+def check_process_section(self, lines, registry, fix_version, progress_bar):
+    """Lint the section of a module between the process definition
     and the 'input:' definition
     Specifically checks for correct software versions
     and containers
+
+    Args:
+        lines (List[str]): Content of process.
+        registry (str): Base Docker registry for containers. Typically quay.io.
+        fix_version (bool): Fix software version
+        progress_bar (ProgressBar): Progress bar to update.
+
+    Returns:
+        Optional[bool]: True if singularity and docker containers match, False otherwise. If process definition does not exist, None.
     """
     # Check that we have a process section
     if len(lines) == 0:
@@ -223,8 +231,8 @@ def check_process_section(self, lines, fix_version, progress_bar):
     self.passed.append(("process_exist", "Process definition exists", self.main_nf))
 
     # Checks that build numbers of bioconda, singularity and docker container are matching
-    singularity_tag = "singularity"
-    docker_tag = "docker"
+    singularity_tag = None
+    docker_tag = None
     bioconda_packages = []
 
     # Process name should be all capital letters
@@ -240,7 +248,12 @@ def check_process_section(self, lines, fix_version, progress_bar):
     # Deprecated enable_conda
     for i, l in enumerate(lines):
         url = None
-        l = l.strip(" '\"")
+        l = l.strip(" \n'\"}:")
+
+        # Catch preceeding "container "
+        if l.startswith("container"):
+            l = l.replace("container", "").strip(" \n'\"}:")
+
         if _container_type(l) == "conda":
             bioconda_packages = [b for b in l.split() if "bioconda::" in b]
             match = re.search(r"params\.enable_conda", l)
@@ -261,9 +274,10 @@ def check_process_section(self, lines, fix_version, progress_bar):
                     )
                 )
         if _container_type(l) == "singularity":
-            # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :" -> v1.2.0_cv1
-            # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :" -> 0.11.9--0
-            match = re.search(r"(?:/)?(?:biocontainers_)?(?::)?([A-Za-z\d\-_.]+?)(?:\.img)?'", l)
+            # e.g. "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img -> v1.2.0_cv1
+            # e.g. "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0 -> 0.11.9--0
+            # Please god let's find a better way to do this than regex
+            match = re.search(r"(?:[:.])?([A-Za-z\d\-_.]+?)(?:\.img)?(?:\.sif)?$", l)
             if match is not None:
                 singularity_tag = match.group(1)
                 self.passed.append(("singularity_tag", f"Found singularity tag: {singularity_tag}", self.main_nf))
@@ -273,16 +287,16 @@ def check_process_section(self, lines, fix_version, progress_bar):
             url = urlparse(l.split("'")[0])
 
         if _container_type(l) == "docker":
-            # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
-            # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
-            match = re.search(r"(?:[/])?(?::)?([A-Za-z\d\-_.]+)'", l)
+            # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5 -> 2.7.1--pl526_5
+            # e.g. "biocontainers/biocontainers:v1.2.0_cv1 -> v1.2.0_cv1
+            match = re.search(r":([A-Za-z\d\-_.]+)$", l)
             if match is not None:
                 docker_tag = match.group(1)
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
-                docker_tag = NoneD
-            if l.startswith("quay.io/"):
+                docker_tag = None
+            if l.startswith(registry):
                 l_stripped = re.sub(r"\W+$", "", l)
                 self.failed.append(
                     (
@@ -297,7 +311,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
             # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
             # If so, add quay.io as default container prefix
             if l.count("/") == 1 and l.count(":") == 1:
-                l = "quay.io/" + l
+                l = "/".join([registry, l]).replace("//", "/")
             url = urlparse(l.split("'")[0])
 
         # lint double quotes
@@ -320,7 +334,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 )
 
         # lint more than one container in the same line
-        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or "quay.io/" in l):
+        if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or l.startswith(registry)):
             self.warned.append(
                 (
                     "container_links",
@@ -412,7 +426,11 @@ def check_process_section(self, lines, fix_version, progress_bar):
             else:
                 self.passed.append(("bioconda_latest", f"Conda package is the latest available: `{bp}`", self.main_nf))
 
-    return docker_tag == singularity_tag
+    # Check if a tag exists at all. If not, return None.
+    if singularity_tag is None or docker_tag is None:
+        return None
+    else:
+        return docker_tag == singularity_tag
 
 
 def check_process_labels(self, lines):
@@ -591,7 +609,7 @@ def _container_type(line):
     """Returns the container type of a build."""
     if line.startswith("conda"):
         return "conda"
-    if line.startswith("https://containers") or line.startswith("https://depot"):
+    if line.startswith("https://") or line.startswith("https://depot"):
         # Look for a http download URL.
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/3809435/713980
         url_regex = (
@@ -601,5 +619,5 @@ def _container_type(line):
         if url_match:
             return "singularity"
         return None
-    if line.count("/") >= 1 and line.count(":") == 1:
+    if line.count("/") >= 1 and line.count(":") == 1 and line.count(" ") == 0 and "https://" not in line:
         return "docker"
diff --git a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
index f93cd55d59..063690f29f 100644
--- a/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
index 9511ea57be..2f83a0962c 100644
--- a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters {%- raw %}
@@ -22,13 +22,18 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
+              "hook_url": "{% raw %}${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}{% endraw %}",
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-${{ github.sha }}{% endraw %}"
             }
           profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
index 6e1fd8c92a..9a0bf4afbc 100644
--- a/nf_core/pipeline-template/.github/workflows/awstest.yml
+++ b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action {%- raw %}
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {
               "outdir": "s3://{% raw %}${{ secrets.AWS_S3_BUCKET }}{% endraw %}/{{ short_name }}/{% raw %}results-test-${{ github.sha }}{% endraw %}"
             }
           profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index bf3dc36bc5..521f3e664a 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md
index 5ac65123ed..e66746dcd5 100644
--- a/nf_core/pipeline-template/README.md
+++ b/nf_core/pipeline-template/README.md
@@ -10,7 +10,7 @@
 {%- 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)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index f8aa90b4e7..e329b3e6fe 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -29,7 +29,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -180,8 +179,9 @@ profiles {
 // Set default registry for Docker and Podman independent of -profile
 // Will not be used unless Docker / Podman are enabled
 // Set to your registry if you have a mirror of containers
-docker.registry = 'quay.io'
-podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
 
 // Nextflow plugins
 plugins {
@@ -214,19 +214,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {
@@ -235,7 +235,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=22.10.1'
+    nextflowVersion = '!>=23.04.0'
     version         = '{{ version }}'
     doi             = ''
 }
diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index c2509faca3..319503c37f 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -249,13 +249,6 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "tracedir": {
-                    "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
diff --git a/nf_core/utils.py b/nf_core/utils.py
index ba0a4fabf3..31738edabe 100644
--- a/nf_core/utils.py
+++ b/nf_core/utils.py
@@ -258,7 +258,7 @@ def fetch_wf_config(wf_path, cache_config=True):
 
     if cache_basedir and cache_fn:
         cache_path = os.path.join(cache_basedir, cache_fn)
-        if os.path.isfile(cache_path):
+        if os.path.isfile(cache_path) and cache_config is True:
             log.debug(f"Found a config cache, loading: {cache_path}")
             with open(cache_path, "r") as fh:
                 try:
@@ -274,7 +274,7 @@ def fetch_wf_config(wf_path, cache_config=True):
         ul = l.decode("utf-8")
         try:
             k, v = ul.split(" = ", 1)
-            config[k] = v
+            config[k] = v.strip("'\"")
         except ValueError:
             log.debug(f"Couldn't find key=value config pair:\n  {ul}")
 
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index b7aaf610ca..d31f2c3212 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -82,6 +82,21 @@ def test_modules_lint_multiple_remotes(self):
     assert len(module_lint.warned) >= 0
 
 
+def test_modules_lint_registry(self):
+    """Test linting the samtools module and alternative registry"""
+    self.mods_install.install("samtools")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
+    module_lint.lint(print_results=False, module="samtools")
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+    module_lint.lint(print_results=False, module="samtools")
+    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
+
+
 def test_modules_lint_patched_modules(self):
     """
     Test creating a patch file and applying it to a new version of the the files
diff --git a/tests/test_download.py b/tests/test_download.py
index 4ee8d3ef6e..332003c426 100644
--- a/tests/test_download.py
+++ b/tests/test_download.py
@@ -128,7 +128,7 @@ def test_wf_use_local_configs(self, tmp_path):
             # Test the function
             download_obj.wf_use_local_configs("workflow")
             wf_config = nf_core.utils.fetch_wf_config(os.path.join(test_outdir, "workflow"), cache_config=False)
-            assert wf_config["params.custom_config_base"] == f"'{test_outdir}/workflow/../configs/'"
+            assert wf_config["params.custom_config_base"] == f"{test_outdir}/workflow/../configs/"
 
     #
     # Tests for 'find_container_images'