Merge pull request #2718 from nf-core/dev

Dev -> Master for 2.12.1

.github/renovate.json5

@@ -14,4 +14,5 @@
             registryUrls: ["docker.io"],
         },
     ],
+    gitIgnoredAuthors: ["[email protected]"],
 }

.github/workflows/changelog.py

@@ -136,12 +136,14 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
     # If the line already contains a link to the PR, don't add it again.
     line = _skip_existing_entry_for_this_pr(line, same_section=False)
 
-    if line.startswith("# ") and not line.strip() == "# nf-core/tools: Changelog":  # Version header, e.g. "# v2.12dev"
+    if (
+        line.startswith("## ") and not line.strip() == "# nf-core/tools: Changelog"
+    ):  # Version header, e.g. "## v2.12dev"
         print(f"Found version header: {line.strip()}")
         updated_lines.append(line)
 
-        # Parse version from the line `# v2.12dev` or
-        # `# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
+        # Parse version from the line `## v2.12dev` or
+        # `## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]` ...
         if not (m := re.match(r".*(v\d+\.\d+(dev)?).*", line)):
             print(f"Cannot parse version from line {line.strip()}.", file=sys.stderr)
             sys.exit(1)

.github/workflows/fix-linting.yml

@@ -10,7 +10,7 @@ jobs:
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
       github.repository == 'nf-core/tools'
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

.github/workflows/pytest.yml

@@ -195,7 +195,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@f30e4959ba63075080d4f7f90cacc18d9f3fafd7 # v4
         with:
           files: coverage.xml
         env:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.1.15
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -1,6 +1,22 @@
 # nf-core/tools: Changelog
 
-# [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.11) - [2024-01-29]
+## [v2.12.1 - Aluminium Wolf - Patch](https://github.com/nf-core/tools/releases/tag/2.12.1) - [2024-02-01]
+
+### Linting
+
+- Handle default values of type number from nextflow schema ([#2703](https://github.com/nf-core/tools/pull/2703))
+- fix ignoring files_unchanged ([#2707](https://github.com/nf-core/tools/pull/2707))
+
+### General
+
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([#2705](https://github.com/nf-core/tools/pull/2705))
+- use types for default value comparison ([#2712](https://github.com/nf-core/tools/pull/2712))
+- fix changelog titles ([#2708](https://github.com/nf-core/tools/pull/2708))
+- Print relative path not absolute path in logo cmd log output ([#2709](https://github.com/nf-core/tools/pull/2709))
+- Update codecov/codecov-action action to v4 ([#2713](https://github.com/nf-core/tools/pull/2713))
+- Ignore nf-core-bot in renovate PRs ([#2716](https://github.com/nf-core/tools/pull/2716))
+
+## [v2.12 - Aluminium Wolf](https://github.com/nf-core/tools/releases/tag/2.12) - [2024-01-29]
 
 ### Template
 
@@ -46,7 +62,7 @@
 - Update peter-evans/create-or-update-comment action to v4 ([#2683](https://github.com/nf-core/tools/pull/2683))
 - Update peter-evans/create-or-update-comment action to v4 ([#2695](https://github.com/nf-core/tools/pull/2695))
 
-# [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
+## [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 
 ### Template
 
@@ -57,7 +73,7 @@
 
 - Only dump `modules.json` when it is modified ([#2609](https://github.com/nf-core/tools/pull/2609))
 
-# [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-19]
+## [v2.11 - Magnesium Dragon](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-19]
 
 ### Template
 
@@ -113,7 +129,7 @@
 - Sort the `installed_by` list in `modules.json` ([#2570](https://github.com/nf-core/tools/pull/2570)).
 - Unset env variable JAVA_TOOL_OPTIONS in gitpod ([#2569](https://github.com/nf-core/tools/pull/2569))
 
-# [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
+## [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 
 ### Template
 
@@ -157,7 +173,7 @@
 - Throw warning when custom workflow name contains special characters ([#2401](https://github.com/nf-core/tools/pull/2401))
 - Bump version of nf-test snapshot files with `nf-core bump-version` ([#2410](https://github.com/nf-core/tools/pull/2410))
 
-# [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]
+## [v2.9 - Chromium Falcon](https://github.com/nf-core/tools/releases/tag/2.9) + [2023-06-29]
 
 ### Template
 
@@ -225,7 +241,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
 - Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312))
 - Add CI tests to test running a pipeline whe it's created from a template skipping different areas
 
-# [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
+## [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
 
 ### Template