From 8c2c995446b69e409b07d0692a52161caa7868a2 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 9 Nov 2023 12:11:53 +0100
Subject: [PATCH 01/29] Ignore ignored config variables

---
 nf_core/lint/nextflow_config.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
index 71c908b7b..24f1e5c12 100644
--- a/nf_core/lint/nextflow_config.py
+++ b/nf_core/lint/nextflow_config.py
@@ -203,6 +203,8 @@ def nextflow_config(self):
 
     # Check the variables that should be set to 'true'
     for k in ["timeline.enabled", "report.enabled", "trace.enabled", "dag.enabled"]:
+        if k in ignore_configs:
+            continue
         if self.nf_config.get(k) == "true":
             passed.append(f"Config ``{k}`` had correct value: ``{self.nf_config.get(k)}``")
         else:

From 4ad4bb70d2eff96d113db9ddee293413e9d317b6 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 9 Nov 2023 13:26:54 +0100
Subject: [PATCH 02/29] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4442f35e5..c84f8fa4f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@
 - Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447))
 - Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448))
 - Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452))
+- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables. ([#2507](https://github.com/nf-core/tools/pull/2507))
 
 ### Modules
 

From e936ac308662d531de27344c9f0fcd23b1e21afc Mon Sep 17 00:00:00 2001
From: Robert Ernst <rfernst@gmail.com>
Date: Mon, 13 Nov 2023 20:05:45 +0100
Subject: [PATCH 03/29] Update CHANGELOG.md
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c84f8fa4f..8d2cecb39 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@
 - Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447))
 - Correctly pass subworkflow linting test if `COMPONENT.out.versions` is used in the script ([#2448](https://github.com/nf-core/tools/pull/2448))
 - Check for spaces in modules container URLs ([#2452](https://github.com/nf-core/tools/issues/2452))
-- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables. ([#2507](https://github.com/nf-core/tools/pull/2507))
+- Correctly ignore `timeline.enabled`, `report.enabled`, `trace.enabled`, `dag.enabled` variables when linting a pipeline. ([#2507](https://github.com/nf-core/tools/pull/2507))
 
 ### Modules
 

From 295a44aba893cc7f430670e334e486d8265475ff Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Nov 2023 14:06:55 +0100
Subject: [PATCH 04/29] fix: use double quotes for interpretable string

---
 nf_core/module-template/modules/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf
index a2cabfd2f..9b9493843 100644
--- a/nf_core/module-template/modules/main.nf
+++ b/nf_core/module-template/modules/main.nf
@@ -27,7 +27,7 @@ process {{ component_name_underscore|upper }} {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
-    conda '${modulesDir}/environment.yml'
+    conda "${modulesDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"

From 7a4ddfce68f9892b44ed1cb0aac856f30bf36abb Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Nov 2023 14:07:18 +0100
Subject: [PATCH 05/29] fix: correct implicit variable name

https://www.nextflow.io/docs/latest/script.html#implicit-variables
---
 nf_core/module-template/modules/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf
index 9b9493843..d482fa0b4 100644
--- a/nf_core/module-template/modules/main.nf
+++ b/nf_core/module-template/modules/main.nf
@@ -27,7 +27,7 @@ process {{ component_name_underscore|upper }} {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
-    conda "${modulesDir}/environment.yml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"

From 1faff58f62aab008652d3659692e234d83fc5ce4 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Nov 2023 14:12:20 +0100
Subject: [PATCH 06/29] docs: describe fix in changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f64047db4..6ae69fc7a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465))
 - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))
 - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
+- Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))
 
 ### Linting
 

From 8f9b8515c55e4d88a1c053f3c7d56588c2be23f1 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 27 Nov 2023 15:38:27 +0100
Subject: [PATCH 07/29] split jobs up to only run once on dev

---
 .github/workflows/pytest.yml | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0fc7f3d09..4d5853499 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -24,7 +24,7 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
-  pytest:
+  setup:
     runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
@@ -34,16 +34,32 @@ jobs:
           - runner: "ubuntu-20.04"
             python-version: "3.8"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v2
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
+
+  test:
+    needs: setup
+    if: ${{ needs.setup.outputs.run-tests == 'true' }}
+    runs-on: ${{ matrix.runner }}
+    steps:
+      - uses: actions/checkout@v2
+        name: Check out source-code repository
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
-        # run full test matrix only on PRs to the master branch
-        if: github.ref == 'refs/heads/master' || matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8'
 
       - name: Install dependencies
         run: |

From 442b17a0e6eedc4f2675e6981c78d72c06958ae8 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 27 Nov 2023 15:44:29 +0100
Subject: [PATCH 08/29] check condition before setting up anything

---
 .github/workflows/pytest.yml | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4d5853499..6886656ca 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -33,19 +33,22 @@ jobs:
         include:
           - runner: "ubuntu-20.04"
             python-version: "3.8"
+
     steps:
-      - uses: actions/checkout@v2
-        name: Check out source-code repository
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
+
+      - name: Check out source-code repository
+        uses: actions/checkout@v4
+        if: ${{ needs.conditions.outputs.run-tests == 'true' }}
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
-
-      - name: Check conditions
-        id: conditions
-        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> $GITHUB_ENV
+        if: ${{ needs.conditions.outputs.run-tests == 'true' }}
 
   test:
     needs: setup

From 26cc37b0e628dbcd02021025abaf71a1adfdd49b Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 27 Nov 2023 15:49:55 +0100
Subject: [PATCH 09/29] fix copy-paste error

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 6886656ca..cd0d58530 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -44,7 +44,7 @@ jobs:
         if: ${{ needs.conditions.outputs.run-tests == 'true' }}
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"

From f54b9f26b966d78a982d37705fbc4b851e641e5d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 27 Nov 2023 16:18:02 +0100
Subject: [PATCH 10/29] fix variable name in lint test

---
 nf_core/modules/lint/environment_yml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index d9c0cbf7f..1367054c8 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -32,7 +32,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf"), "r") as fh:
             main_nf = fh.read()
-            if "conda '${modulesDir}/environment.yml'" in main_nf:
+            if "conda '${moduleDir}/environment.yml'" in main_nf:
                 module.failed.append(
                     ("environment_yml_exists", "Module's `environment.yml` does not exist", module.environment_yml)
                 )

From 36ec7930c6de9bc7fdda7313a3a0befc1e2a8ae0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Mon, 27 Nov 2023 16:36:47 +0100
Subject: [PATCH 11/29] fix incorrectly guessed syntax

---
 .github/workflows/pytest.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index cd0d58530..340768b83 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -41,14 +41,16 @@ jobs:
 
       - name: Check out source-code repository
         uses: actions/checkout@v4
-        if: ${{ needs.conditions.outputs.run-tests == 'true' }}
+        if: ${{ steps.conditions.outputs.run-tests == 'true' }}
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
-        if: ${{ needs.conditions.outputs.run-tests == 'true' }}
+        if: ${{ steps.conditions.outputs.run-tests == 'true' }}
+    outputs:
+      run-tests: ${{ env.run-tests }}
 
   test:
     needs: setup

From 84f92bc09c1ba167403656c32b2046402bef5079 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Mon, 27 Nov 2023 18:52:23 +0100
Subject: [PATCH 12/29] fix: adjust quotes to match template

---
 nf_core/modules/lint/environment_yml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
index 1367054c8..a05242553 100644
--- a/nf_core/modules/lint/environment_yml.py
+++ b/nf_core/modules/lint/environment_yml.py
@@ -32,7 +32,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf"), "r") as fh:
             main_nf = fh.read()
-            if "conda '${moduleDir}/environment.yml'" in main_nf:
+            if 'conda "${moduleDir}/environment.yml"' in main_nf:
                 module.failed.append(
                     ("environment_yml_exists", "Module's `environment.yml` does not exist", module.environment_yml)
                 )

From d2c5400877b2458a9c7faeef183f553cd64f05d9 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 14:17:14 +0100
Subject: [PATCH 13/29] add mypy to pre-commit config, fix mypy errors

---
 .pre-commit-config.yaml               | 10 +++++
 docs/api/_src/conf.py                 |  5 ++-
 mypy.ini                              |  1 +
 nf_core/__main__.py                   | 56 +++++++++++++--------------
 nf_core/params_file.py                |  2 +-
 nf_core/subworkflows/lint/__init__.py | 12 +++---
 pyproject.toml                        |  5 ---
 requirements-dev.txt                  |  1 +
 tests/test_lint.py                    | 20 +++++-----
 9 files changed, 58 insertions(+), 54 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b7aeeb5bc..578d17f76 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -11,3 +11,13 @@ repos:
     rev: "v2.7.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.7.1" # Use the sha / tag you want to point at
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - types-PyYAML
+          - types-requests
+          - types-jsonschema
+          - types-Markdown
+          - types-setuptools
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
index 4d8ae661d..27eaf9bcb 100644
--- a/docs/api/_src/conf.py
+++ b/docs/api/_src/conf.py
@@ -14,6 +14,7 @@
 #
 import os
 import sys
+from typing import Dict
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
 import nf_core
@@ -58,7 +59,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language: str = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -113,7 +114,7 @@
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: Dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
diff --git a/mypy.ini b/mypy.ini
index f869fa7e4..c48aa5884 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,2 +1,3 @@
 [mypy]
 warn_unused_configs = True
+ignore_missing_imports = true
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 232f1bf11..ec5ddeeaa 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -151,7 +151,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 
 
 # nf-core list
-@nf_core_cli.command()
+@nf_core_cli.command("list")
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option(
     "-s",
@@ -162,7 +162,7 @@ def nf_core_cli(ctx, verbose, hide_progress, log_file):
 )
 @click.option("--json", is_flag=True, default=False, help="Print full output as JSON")
 @click.option("--show-archived", is_flag=True, default=False, help="Print archived workflows")
-def list(keywords, sort, json, show_archived):
+def list_pipelines(keywords, sort, json, show_archived):
     """
     List available nf-core pipelines with local info.
 
@@ -553,9 +553,9 @@ def subworkflows(ctx, git_remote, branch, no_pull):
 
 
 # nf-core modules list subcommands
-@modules.group()
+@modules.group("list")
 @click.pass_context
-def list(ctx):
+def modules_list(ctx):
     """
     List modules in a local pipeline or remote repository.
     """
@@ -563,11 +563,11 @@ def list(ctx):
 
 
 # nf-core modules list remote
-@list.command()
+@modules_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def remote(ctx, keywords, json):
+def modules_list_remote(ctx, keywords, json):
     """
     List modules in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
@@ -588,7 +588,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core modules list local
-@list.command()
+@modules_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -599,7 +599,7 @@ def remote(ctx, keywords, json):
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     """
     List modules installed locally in a pipeline
     """
@@ -620,7 +620,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core modules install
-@modules.command()
+@modules.command("install")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -633,7 +633,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 @click.option("-p", "--prompt", is_flag=True, default=False, help="Prompt for the version of the module")
 @click.option("-f", "--force", is_flag=True, default=False, help="Force reinstallation of module if it already exists")
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install module at commit SHA")
-def install(ctx, tool, dir, prompt, force, sha):
+def modules_install(ctx, tool, dir, prompt, force, sha):
     """
     Install DSL2 modules within a pipeline.
 
@@ -660,7 +660,7 @@ def install(ctx, tool, dir, prompt, force, sha):
 
 
 # nf-core modules update
-@modules.command()
+@modules.command("update")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -699,7 +699,7 @@ def install(ctx, tool, dir, prompt, force, sha):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
+def modules_update(ctx, tool, directory, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 modules within a pipeline.
 
@@ -767,7 +767,7 @@ def patch(ctx, tool, dir, remove):
 
 
 # nf-core modules remove
-@modules.command()
+@modules.command("remove")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -777,7 +777,7 @@ def patch(ctx, tool, dir, remove):
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def remove(ctx, dir, tool):
+def modules_remove(ctx, dir, tool):
     """
     Remove a module from a pipeline.
     """
@@ -887,7 +887,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
 
 
 # nf-core modules lint
-@modules.command()
+@modules.command("lint")
 @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>")
@@ -912,9 +912,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
     show_default=True,
 )
 @click.option("--fix-version", is_flag=True, help="Fix the module version if a newer version is available")
-def lint(
-    ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version
-):  # pylint: disable=redefined-outer-name
+def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed, sort_by, fix_version):
     """
     Lint one or more modules in a directory.
 
@@ -959,7 +957,7 @@ def lint(
 
 
 # nf-core modules info
-@modules.command()
+@modules.command("info")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
@@ -969,7 +967,7 @@ def lint(
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def info(ctx, tool, dir):
+def modules_info(ctx, tool, dir):
     """
     Show developer usage information about a given module.
 
@@ -1095,9 +1093,9 @@ def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once):
 
 
 # nf-core subworkflows list subcommands
-@subworkflows.group()
+@subworkflows.group("list")
 @click.pass_context
-def list(ctx):
+def subworkflows_list(ctx):
     """
     List subworkflows in a local pipeline or remote repository.
     """
@@ -1105,7 +1103,7 @@ def list(ctx):
 
 
 # nf-core subworkflows list remote
-@list.command()
+@subworkflows_list.command("remote")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -1131,7 +1129,7 @@ def remote(ctx, keywords, json):
 
 
 # nf-core subworkflows list local
-@list.command()
+@subworkflows_list.command("local")
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
@@ -1163,7 +1161,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
 
 
 # nf-core subworkflows lint
-@subworkflows.command()
+@subworkflows.command("lint")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<pipeline/modules directory>")
@@ -1187,9 +1185,7 @@ def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     help="Sort lint output by subworkflow or test name.",
     show_default=True,
 )
-def lint(
-    ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by
-):  # pylint: disable=redefined-outer-name
+def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by):
     """
     Lint one or more subworkflows in a directory.
 
@@ -1496,11 +1492,11 @@ def build(dir, no_prompts, web_only, url):
 
 
 # nf-core schema lint
-@schema.command()
+@schema.command("lint")
 @click.argument(
     "schema_path", type=click.Path(exists=True), default="nextflow_schema.json", metavar="<pipeline schema>"
 )
-def lint(schema_path):
+def schema_lint(schema_path):
     """
     Check that a given pipeline schema is valid.
 
diff --git a/nf_core/params_file.py b/nf_core/params_file.py
index 39986b95c..5c50c53fb 100644
--- a/nf_core/params_file.py
+++ b/nf_core/params_file.py
@@ -89,7 +89,7 @@ def __init__(
         self,
         pipeline=None,
         revision=None,
-    ):
+    ) -> None:
         """Initialise the ParamFileBuilder class
 
         Args:
diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py
index 44c7c21a3..ffba41f9d 100644
--- a/nf_core/subworkflows/lint/__init__.py
+++ b/nf_core/subworkflows/lint/__init__.py
@@ -29,12 +29,12 @@ class SubworkflowLint(ComponentLint):
     """
 
     # Import lint functions
-    from .main_nf import main_nf
-    from .meta_yml import meta_yml
-    from .subworkflow_changes import subworkflow_changes
-    from .subworkflow_tests import subworkflow_tests
-    from .subworkflow_todos import subworkflow_todos
-    from .subworkflow_version import subworkflow_version
+    from .main_nf import main_nf  # type: ignore[misc]
+    from .meta_yml import meta_yml  # type: ignore[misc]
+    from .subworkflow_changes import subworkflow_changes  # type: ignore[misc]
+    from .subworkflow_tests import subworkflow_tests  # type: ignore[misc]
+    from .subworkflow_todos import subworkflow_todos  # type: ignore[misc]
+    from .subworkflow_version import subworkflow_version  # type: ignore[misc]
 
     def __init__(
         self,
diff --git a/pyproject.toml b/pyproject.toml
index f0702742f..238007310 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,8 +20,3 @@ norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".githu
 profile = "black"
 known_first_party = ["nf_core"]
 multi_line_output = 3
-
-[tool.mypy]
-ignore_missing_imports = true
-follow_imports = "skip"
-disable_error_code = "no-redef"
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 12183eb98..3ef059308 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -11,3 +11,4 @@ types-PyYAML
 types-requests
 types-jsonschema
 types-Markdown
+types-setuptools
diff --git a/tests/test_lint.py b/tests/test_lint.py
index 67104e3ad..69917b279 100644
--- a/tests/test_lint.py
+++ b/tests/test_lint.py
@@ -178,44 +178,44 @@ def test_sphinx_md_files(self):
     #######################
     # SPECIFIC LINT TESTS #
     #######################
-    from .lint.actions_awsfulltest import (
+    from .lint.actions_awsfulltest import (  # type: ignore[misc]
         test_actions_awsfulltest_fail,
         test_actions_awsfulltest_pass,
         test_actions_awsfulltest_warn,
     )
-    from .lint.actions_awstest import (
+    from .lint.actions_awstest import (  # type: ignore[misc]
         test_actions_awstest_fail,
         test_actions_awstest_pass,
     )
-    from .lint.actions_ci import (
+    from .lint.actions_ci import (  # type: ignore[misc]
         test_actions_ci_fail_wrong_nf,
         test_actions_ci_fail_wrong_trigger,
         test_actions_ci_pass,
     )
-    from .lint.actions_schema_validation import (
+    from .lint.actions_schema_validation import (  # type: ignore[misc]
         test_actions_schema_validation_fails_for_additional_property,
         test_actions_schema_validation_missing_jobs,
         test_actions_schema_validation_missing_on,
     )
-    from .lint.files_exist import (
+    from .lint.files_exist import (  # type: ignore[misc]
         test_files_exist_depreciated_file,
         test_files_exist_missing_config,
         test_files_exist_missing_main,
         test_files_exist_pass,
     )
-    from .lint.files_unchanged import (
+    from .lint.files_unchanged import (  # type: ignore[misc]
         test_files_unchanged_fail,
         test_files_unchanged_pass,
     )
-    from .lint.merge_markers import test_merge_markers_found
-    from .lint.modules_json import test_modules_json_pass
-    from .lint.nextflow_config import (
+    from .lint.merge_markers import test_merge_markers_found  # type: ignore[misc]
+    from .lint.modules_json import test_modules_json_pass  # type: ignore[misc]
+    from .lint.nextflow_config import (  # type: ignore[misc]
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,
         test_nextflow_config_missing_test_profile_failed,
     )
-    from .lint.version_consistency import test_version_consistency
+    from .lint.version_consistency import test_version_consistency  # type: ignore[misc]
 
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2

From 62ee35e4d44339569206f79437a3a5076b7db175 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 14:37:52 +0100
Subject: [PATCH 14/29] try different condition and without accessing the
 matrix

---
 .github/workflows/pytest.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 340768b83..03d5bc65e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -41,29 +41,31 @@ jobs:
 
       - name: Check out source-code repository
         uses: actions/checkout@v4
-        if: ${{ steps.conditions.outputs.run-tests == 'true' }}
+        if: ${{ env.run-tests == 'true' }}
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
-        if: ${{ steps.conditions.outputs.run-tests == 'true' }}
+        if: ${{ env.run-tests == 'true' }}
     outputs:
+      python-version: ${{ matrix.python-version }}
+      runner: ${{ matrix.runner }}
       run-tests: ${{ env.run-tests }}
 
   test:
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ matrix.runner }}
+    runs-on: ${{ needs.setup.outputs.runner }}
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ needs.setup.outputs.python-version }}
         uses: actions/setup-python@v2
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
 
       - name: Install dependencies
@@ -72,7 +74,7 @@ jobs:
           pip install -e .
 
       - name: Downgrade git to the Ubuntu official repository's version
-        if: ${{ matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8' }}
+        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
         run: |
           sudo apt update
           sudo apt remove git git-man

From b442d50adc5ec9b87ca045eb23dca4be5b5d9212 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 15:01:11 +0100
Subject: [PATCH 15/29] use same naming for modules and subworkflo commands

---
 nf_core/__main__.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index ec5ddeeaa..43095bc19 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1107,7 +1107,7 @@ def subworkflows_list(ctx):
 @click.pass_context
 @click.argument("keywords", required=False, nargs=-1, metavar="<filter keywords>")
 @click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
-def remote(ctx, keywords, json):
+def subworkflows_list_remote(ctx, keywords, json):
     """
     List subworkflows in a remote GitHub repo [dim i](e.g [link=https://github.com/nf-core/modules]nf-core/modules[/])[/].
     """
@@ -1140,7 +1140,7 @@ def remote(ctx, keywords, json):
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
+def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-builtin
     """
     List subworkflows installed locally in a pipeline
     """
@@ -1229,7 +1229,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
 
 
 # nf-core subworkflows info
-@subworkflows.command()
+@subworkflows.command("info")
 @click.pass_context
 @click.argument("tool", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1239,7 +1239,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def info(ctx, tool, dir):
+def subworkflows_info(ctx, tool, dir):
     """
     Show developer usage information about a given subworkflow.
 
@@ -1268,7 +1268,7 @@ def info(ctx, tool, dir):
 
 
 # nf-core subworkflows install
-@subworkflows.command()
+@subworkflows.command("install")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1283,7 +1283,7 @@ def info(ctx, tool, dir):
     "-f", "--force", is_flag=True, default=False, help="Force reinstallation of subworkflow if it already exists"
 )
 @click.option("-s", "--sha", type=str, metavar="<commit sha>", help="Install subworkflow at commit SHA")
-def install(ctx, subworkflow, dir, prompt, force, sha):
+def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
     """
     Install DSL2 subworkflow within a pipeline.
 
@@ -1310,7 +1310,7 @@ def install(ctx, subworkflow, dir, prompt, force, sha):
 
 
 # nf-core subworkflows remove
-@subworkflows.command()
+@subworkflows.command("remove")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1320,7 +1320,7 @@ def install(ctx, subworkflow, dir, prompt, force, sha):
     default=".",
     help=r"Pipeline directory. [dim]\[default: current working directory][/]",
 )
-def remove(ctx, dir, subworkflow):
+def subworkflows_remove(ctx, dir, subworkflow):
     """
     Remove a subworkflow from a pipeline.
     """
@@ -1340,7 +1340,7 @@ def remove(ctx, dir, subworkflow):
 
 
 # nf-core subworkflows update
-@subworkflows.command()
+@subworkflows.command("update")
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option(
@@ -1378,7 +1378,7 @@ def remove(ctx, dir, subworkflow):
     default=False,
     help="Automatically update all linked modules and subworkflows without asking for confirmation",
 )
-def update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
+def subworkflows_update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save_diff, update_deps):
     """
     Update DSL2 subworkflow within a pipeline.
 
@@ -1392,7 +1392,7 @@ def update(ctx, subworkflow, dir, force, prompt, sha, install_all, preview, save
             force,
             prompt,
             sha,
-            all,
+            install_all,
             preview,
             save_diff,
             update_deps,

From ed8efbcea8e0b13d508c9229c82fc8412a3acc63 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 15:53:34 +0100
Subject: [PATCH 16/29] update github checkout and setup-python

---
 .github/workflows/create-lint-wf.yml             |  4 ++--
 .../workflows/create-test-lint-wf-template.yml   |  4 ++--
 .github/workflows/create-test-wf.yml             |  2 +-
 .github/workflows/deploy-pypi.yml                |  2 +-
 .github/workflows/fix-linting.yml                |  4 ++--
 .github/workflows/lint-code.yml                  | 16 ++++++++--------
 .github/workflows/push_dockerhub_dev.yml         |  2 +-
 .github/workflows/push_dockerhub_release.yml     |  2 +-
 .github/workflows/pytest.yml                     |  2 +-
 .github/workflows/rich-codex.yml                 |  2 +-
 .github/workflows/sync.yml                       |  4 ++--
 .github/workflows/tools-api-docs-dev.yml         |  2 +-
 .github/workflows/tools-api-docs-release.yml     |  2 +-
 CHANGELOG.md                                     |  1 +
 .../pipeline-template/.github/workflows/ci.yml   |  2 +-
 .../.github/workflows/fix-linting.yml            |  4 ++--
 .../.github/workflows/linting.yml                | 12 ++++++------
 17 files changed, 34 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index d5f377a48..51daec21b 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -27,7 +27,7 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
@@ -48,7 +48,7 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 5ce9b4111..f1c6c4d14 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -33,7 +33,7 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
@@ -52,7 +52,7 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index d96518d7c..4f66adae6 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -26,7 +26,7 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
index 9b46f0731..b847df921 100644
--- a/.github/workflows/deploy-pypi.yml
+++ b/.github/workflows/deploy-pypi.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python 3.12
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index f56cb927f..a6cf14956 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index a951230a6..baaaedcb4 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -16,9 +16,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -30,9 +30,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -43,7 +43,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -74,7 +74,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
@@ -89,8 +89,8 @@ jobs:
   static-type-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.12
           cache: "pip"
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index dea28cdd3..169a917d8 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev
diff --git a/.github/workflows/push_dockerhub_release.yml b/.github/workflows/push_dockerhub_release.yml
index 857b24102..49ce17dd8 100644
--- a/.github/workflows/push_dockerhub_release.yml
+++ b/.github/workflows/push_dockerhub_release.yml
@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0fc7f3d09..be9942dd1 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -34,7 +34,7 @@ jobs:
           - runner: "ubuntu-20.04"
             python-version: "3.8"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       - name: Set up Python ${{ matrix.python-version }}
diff --git a/.github/workflows/rich-codex.yml b/.github/workflows/rich-codex.yml
index 54aaf240d..836825539 100644
--- a/.github/workflows/rich-codex.yml
+++ b/.github/workflows/rich-codex.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 5e7719973..b8fb28794 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -36,10 +36,10 @@ jobs:
       matrix: ${{fromJson(needs.get-pipelines.outputs.matrix)}}
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/tools
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out nf-core/${{ matrix.pipeline }}
         with:
           repository: nf-core/${{ matrix.pipeline }}
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 3a4725a94..7de8913e0 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -24,7 +24,7 @@ jobs:
 
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml
index 8a6eda131..412784c23 100644
--- a/.github/workflows/tools-api-docs-release.yml
+++ b/.github/workflows/tools-api-docs-release.yml
@@ -19,7 +19,7 @@ jobs:
           - ${{ github.event.release.tag_name }}
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6ae69fc7a..0ab328866 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@
 - Change testing framework for modules and subworkflows from pytest to nf-test ([#2490](https://github.com/nf-core/tools/pull/2490))
 - `bump_version` keeps now the indentation level of the updated version entries ([#2514](https://github.com/nf-core/tools/pull/2514))
 - Run tests with Python 3.12 ([#2522](https://github.com/nf-core/tools/pull/2522)).
+- Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545))
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 
diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml
index 521f3e664..3edd49f09 100644
--- a/nf_core/pipeline-template/.github/workflows/ci.yml
+++ b/nf_core/pipeline-template/.github/workflows/ci.yml
@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index f3dc3e50f..31e8cd2b3 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index edce89065..64d1851f2 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

From ae505c46cd271582c50aa956bfbc9449222bcab4 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 16:01:22 +0100
Subject: [PATCH 17/29] =?UTF-8?q?switch=20to=20self-hosted=20=F0=9F=A4=9E?=
 =?UTF-8?q?=F0=9F=8F=BB?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 03d5bc65e..b6edac518 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -57,7 +57,7 @@ jobs:
   test:
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository

From 1ad27a7eb955a13dcc5dc53ab576be94c7429126 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 16:05:26 +0100
Subject: [PATCH 18/29] =?UTF-8?q?Revert=20"switch=20to=20self-hosted=20?=
 =?UTF-8?q?=F0=9F=A4=9E=F0=9F=8F=BB"?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This reverts commit ae505c46cd271582c50aa956bfbc9449222bcab4.
---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b6edac518..03d5bc65e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -57,7 +57,7 @@ jobs:
   test:
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ["self-hosted"]
+    runs-on: ${{ needs.setup.outputs.runner }}
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository

From 13bbac6570af595697aaec638a82d7e7fd4fa3ac Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 16:32:57 +0100
Subject: [PATCH 19/29] fix subworkflow command

---
 nf_core/__main__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 232f1bf11..81e7de0f1 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -1064,7 +1064,6 @@ def create_subworkflow(ctx, subworkflow, dir, author, force):
 @click.pass_context
 @click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
 @click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<nf-core/modules directory>")
-@click.option("-t", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
 @click.option("-p", "--no-prompts", is_flag=True, default=False, help="Use defaults without prompting")
 @click.option("-u", "--update", is_flag=True, default=False, help="Update existing snapshots")
 @click.option("-o", "--once", is_flag=True, default=False, help="Run tests only once. Don't check snapshot stability")

From ad03acdd8007e482f7f6d1df2dd9b3b9394ab103 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 28 Nov 2023 22:00:46 +0100
Subject: [PATCH 20/29] fix parsing for include statement of nested
 subworkflows, print long messages

---
 nf_core/components/lint/__init__.py            | 17 ++++++++++++-----
 nf_core/components/nfcore_component.py         | 13 ++++++++++---
 nf_core/subworkflows/lint/subworkflow_tests.py |  1 +
 3 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
index c46d68ff2..efffc28e8 100644
--- a/nf_core/components/lint/__init__.py
+++ b/nf_core/components/lint/__init__.py
@@ -10,7 +10,9 @@
 import os
 from pathlib import Path
 
-import rich
+import rich.box
+import rich.console
+import rich.panel
 from rich.markdown import Markdown
 from rich.table import Table
 
@@ -209,7 +211,7 @@ def _print_results(self, show_passed=False, sort_by="test"):
         self.failed.sort(key=operator.attrgetter(*sort_order))
 
         # Find maximum module name length
-        max_name_len = 40
+        max_name_len = len(self.component_type[:-1] + " name")
         for tests in [self.passed, self.warned, self.failed]:
             try:
                 for lint_result in tests:
@@ -264,7 +266,7 @@ def format_result(test_results, table):
             table = Table(style="yellow", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.warned, table)
             console.print(
                 rich.panel.Panel(
@@ -278,10 +280,15 @@ def format_result(test_results, table):
 
         # Table of failing tests
         if len(self.failed) > 0:
-            table = Table(style="red", box=rich.box.MINIMAL, pad_edge=False, border_style="dim")
+            table = Table(
+                style="red",
+                box=rich.box.MINIMAL,
+                pad_edge=False,
+                border_style="dim",
+            )
             table.add_column(f"{self.component_type[:-1].title()} name", width=max_name_len)
             table.add_column("File path")
-            table.add_column("Test message")
+            table.add_column("Test message", overflow="fold")
             table = format_result(self.failed, table)
             console.print(
                 rich.panel.Panel(
diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 190310faa..8d9b6840b 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -4,6 +4,7 @@
 import logging
 import re
 from pathlib import Path
+from typing import Union
 
 log = logging.getLogger(__name__)
 
@@ -77,7 +78,7 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
-    def _get_main_nf_tags(self, test_main_nf: str):
+    def _get_main_nf_tags(self, test_main_nf: Union[Path, str]):
         """Collect all tags from the main.nf.test file."""
         tags = []
         with open(test_main_nf, "r") as fh:
@@ -86,13 +87,19 @@ def _get_main_nf_tags(self, test_main_nf: str):
                     tags.append(line.strip().split()[1].strip('"'))
         return tags
 
-    def _get_included_components(self, main_nf: str):
+    def _get_included_components(self, main_nf: Union[Path, str]):
         """Collect all included components from the main.nf file."""
         included_components = []
         with open(main_nf, "r") as fh:
             for line in fh:
                 if line.strip().startswith("include"):
-                    included_components.append(line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/"))
+                    # get tool/subtool or subworkflow name from include statement, can be in the form
+                    #'../../../modules/nf-core/hisat2/align/main'
+                    #'../bam_sort_stats_samtools/main'
+                    #'../subworkflows/nf-core/bam_sort_stats_samtools/main'
+                    component = line.strip().split()[-1].split(self.org)[-1].split("main")[0].strip("/")
+                    component = component.replace("'../", "subworkflows/")
+                    included_components.append(component)
         return included_components
 
     def get_inputs_from_main_nf(self):
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index e82d00f63..30439a8d0 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -107,6 +107,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
             included_components = []
             if subworkflow.main_nf.is_file():
                 included_components = subworkflow._get_included_components(subworkflow.main_nf)
+            log.debug(f"Required tags: {required_tags}")
             missing_tags = []
             for tag in required_tags + included_components:
                 if tag not in main_nf_tags:

From da7636a3e44ead54ffacce02f20dd175cc06121a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 13:25:03 +0100
Subject: [PATCH 21/29] fix subworkflow tag in template

---
 nf_core/subworkflow-template/subworkflows/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
index b0a212f2a..59c4fdb67 100644
--- a/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
+++ b/nf_core/subworkflow-template/subworkflows/tests/main.nf.test
@@ -8,7 +8,6 @@ nextflow_workflow {
 
     tag "subworkflows"
     tag "subworkflows_nfcore"
-    tag "{{ component_name }}"
     tag "subworkflows/{{ component_name }}"
     // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
     tag "samtools"

From cc3b6e1b9b15fb2b2bbbcb1bcd8eb521669e0182 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 15:59:14 +0100
Subject: [PATCH 22/29] fix linting tests

---
 .github/workflows/pytest.yml                  |  1 +
 .../subworkflows/lint/subworkflow_tests.py    |  1 -
 tests/subworkflows/lint.py                    | 11 +++++++----
 tests/test_subworkflows.py                    | 19 ++++++++-----------
 4 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 03d5bc65e..2557c4fa4 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -55,6 +55,7 @@ jobs:
       run-tests: ${{ env.run-tests }}
 
   test:
+    name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
     runs-on: ${{ needs.setup.outputs.runner }}
diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
index 30439a8d0..a125be152 100644
--- a/nf_core/subworkflows/lint/subworkflow_tests.py
+++ b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -102,7 +102,6 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
                 "subworkflows",
                 f"subworkflows/{subworkflow.component_name}",
                 "subworkflows_nfcore",
-                subworkflow.component_name,
             ]
             included_components = []
             if subworkflow.main_nf.is_file():
diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py
index 5bbe746f2..1380db226 100644
--- a/tests/subworkflows/lint.py
+++ b/tests/subworkflows/lint.py
@@ -28,9 +28,8 @@ def test_subworkflows_lint_new_subworkflow(self):
     """lint a new subworkflow"""
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=True, all_subworkflows=True)
-    assert (
-        len(subworkflow_lint.failed) == 1  # test snap missing after creating a subworkflow
-    ), f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+    assert len(subworkflow_lint.failed) == 0
+
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
 
@@ -68,7 +67,6 @@ def test_subworkflows_lint_multiple_remotes(self):
 
 def test_subworkflows_lint_snapshot_file(self):
     """Test linting a subworkflow with a snapshot file"""
-    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
@@ -78,8 +76,10 @@ def test_subworkflows_lint_snapshot_file(self):
 
 def test_subworkflows_lint_snapshot_file_missing_fail(self):
     """Test linting a subworkflow with a snapshot file missing, which should fail"""
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
@@ -96,8 +96,11 @@ def test_subworkflows_lint_snapshot_file_not_needed(self):
         Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test"), "w"
     ) as fh:
         fh.write(new_content)
+
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").unlink()
     subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules)
     subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow")
+    Path(self.nfcore_modules, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
     assert len(subworkflow_lint.passed) > 0
     assert len(subworkflow_lint.warned) >= 0
diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py
index 33cad81e3..a4ab959fb 100644
--- a/tests/test_subworkflows.py
+++ b/tests/test_subworkflows.py
@@ -4,6 +4,7 @@
 import os
 import shutil
 import unittest
+from pathlib import Path
 
 import nf_core.create
 import nf_core.modules
@@ -21,22 +22,18 @@
 def create_modules_repo_dummy(tmp_dir):
     """Create a dummy copy of the nf-core/modules repo"""
 
-    root_dir = os.path.join(tmp_dir, "modules")
-    os.makedirs(os.path.join(root_dir, "modules"))
-    os.makedirs(os.path.join(root_dir, "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "subworkflows", "nf-core"))
-    os.makedirs(os.path.join(root_dir, "tests", "modules"))
-    os.makedirs(os.path.join(root_dir, "tests", "subworkflows"))
-    os.makedirs(os.path.join(root_dir, "tests", "config"))
-    with open(os.path.join(root_dir, "tests", "config", "pytest_modules.yml"), "w") as fh:
-        fh.writelines(["test:", "\n  - modules/test/**", "\n  - tests/modules/test/**"])
-    with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
+    root_dir = Path(tmp_dir, "modules")
+    Path(root_dir, "modules").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "subworkflows", "nf-core").mkdir(parents=True, exist_ok=True)
+    Path(root_dir, "tests", "config").mkdir(parents=True, exist_ok=True)
+    with open(Path(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
-
     # TODO Add a mock here
     subworkflow_create = nf_core.subworkflows.SubworkflowCreate(root_dir, "test_subworkflow", "@author", True)
     subworkflow_create.create()
 
+    Path(root_dir, "subworkflows", "nf-core", "test_subworkflow", "tests", "main.nf.test.snap").touch()
     return root_dir
 
 

From c6ff441dca15da1162d2018ea063dc76d4073dc5 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:13:04 +0100
Subject: [PATCH 23/29] try once more on self hosted

---
 .github/workflows/pytest.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 2557c4fa4..573c1364b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ${{ needs.setup.outputs.runner }}
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -80,7 +80,7 @@ jobs:
           sudo apt update
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
-          sudo apt install git
+          sudo apt install -y git
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV

From ffba25fa46cda05931e72f0a6cfcabe9a131f099 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:22:32 +0100
Subject: [PATCH 24/29] run even more things on aws

---
 .github/workflows/lint-code.yml | 10 +++++-----
 .github/workflows/pytest.yml    |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index baaaedcb4..b348496c3 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -14,7 +14,7 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -28,7 +28,7 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -41,7 +41,7 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
 
@@ -71,7 +71,7 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - name: Check out source-code repository
         uses: actions/checkout@v4
@@ -87,7 +87,7 @@ jobs:
           requirementsFiles: "requirements.txt requirements-dev.txt"
 
   static-type-check:
-    runs-on: ubuntu-latest
+    runs-on: ["self-hosted"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 573c1364b..4f370bc28 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -25,7 +25,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ${{ matrix.runner }}
+    runs-on: ["self-hosted"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]

From d64c3b9aa5e1a6523f5e2c5ea137723a6355d36d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:26:11 +0100
Subject: [PATCH 25/29] fix node setup

---
 .github/workflows/lint-code.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index b348496c3..168fac653 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -19,6 +19,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -33,6 +35,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

From 7f6bc73b7577547c28bc6041a8a0d11b4bcb651d Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 16:37:17 +0100
Subject: [PATCH 26/29] fix apt command

---
 .github/workflows/pytest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 4f370bc28..c6de90d93 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -78,7 +78,7 @@ jobs:
         if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
         run: |
           sudo apt update
-          sudo apt remove git git-man
+          sudo apt remove -y git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install -y git
       - name: Get current date

From a84d064d2ade1412d8704d72879692d02d3a7dde Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 17:16:49 +0100
Subject: [PATCH 27/29] reset aws runner for nf-test related things, try it
 with other workflows

---
 .github/workflows/create-lint-wf.yml               | 4 +++-
 .github/workflows/create-test-lint-wf-template.yml | 4 +++-
 .github/workflows/create-test-wf.yml               | 2 +-
 .github/workflows/fix-linting.yml                  | 2 ++
 .github/workflows/push_dockerhub_dev.yml           | 2 +-
 .github/workflows/pytest.yml                       | 2 +-
 .github/workflows/tools-api-docs-dev.yml           | 2 +-
 7 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 51daec21b..a3941f3ce 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   MakeTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -49,6 +49,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index f1c6c4d14..b14a0fac5 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -20,7 +20,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
@@ -53,6 +53,8 @@ jobs:
 
       # Install the Prettier linting tools
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 4f66adae6..7b6a868f9 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index a6cf14956..d84615120 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -25,6 +25,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/.github/workflows/push_dockerhub_dev.yml b/.github/workflows/push_dockerhub_dev.yml
index 169a917d8..1230bfc9d 100644
--- a/.github/workflows/push_dockerhub_dev.yml
+++ b/.github/workflows/push_dockerhub_dev.yml
@@ -13,7 +13,7 @@ concurrency:
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
     # Only run for the nf-core repo, for releases and merged PRs
     if: ${{ github.repository == 'nf-core/tools' }}
     env:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index c6de90d93..0561be25e 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -58,7 +58,7 @@ jobs:
     name: Test with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: setup
     if: ${{ needs.setup.outputs.run-tests == 'true' }}
-    runs-on: ["self-hosted"]
+    runs-on: ${{ needs.setup.outputs.runner }}
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml
index 7de8913e0..f6106bd8b 100644
--- a/.github/workflows/tools-api-docs-dev.yml
+++ b/.github/workflows/tools-api-docs-dev.yml
@@ -20,7 +20,7 @@ concurrency:
 jobs:
   api-docs:
     name: Build & push Sphinx API docs
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
 
     steps:
       - name: Check out source-code repository

From 9599287f7fe67fab93e57dee4a4dc67c8a91eec0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 17:24:01 +0100
Subject: [PATCH 28/29] try fixing aws runs

---
 nf_core/pipeline-template/nextflow.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6a6bee6a8..31917a3e3 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -121,6 +121,7 @@ profiles {
         shifter.enabled        = false
         charliecloud.enabled   = false
         apptainer.enabled      = false
+        runOptions             = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'

From 88e8bce12ac8c967e0fc36e153388f6f772e0c47 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Wed, 29 Nov 2023 23:18:08 +0100
Subject: [PATCH 29/29] run on github runners

---
 .github/workflows/create-test-lint-wf-template.yml | 2 +-
 .github/workflows/create-test-wf.yml               | 2 +-
 .github/workflows/pytest.yml                       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index b14a0fac5..4be309862 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -20,7 +20,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
index 7b6a868f9..4f66adae6 100644
--- a/.github/workflows/create-test-wf.yml
+++ b/.github/workflows/create-test-wf.yml
@@ -17,7 +17,7 @@ env:
 
 jobs:
   RunTestWorkflow:
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     env:
       NXF_ANSI_LOG: false
     strategy:
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 0561be25e..9f8172a3b 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -25,7 +25,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ["self-hosted"]
+    runs-on: ["ubuntu-latest"]
     strategy:
       matrix:
         python-version: ["3.8", "3.12"]