Merge branch 'dev' into renovate/textual-dev-1.x

Author: mirpedrol

.github/actions/create-lint-wf/action.yml

@@ -15,7 +15,6 @@ runs:
         cd create-lint-wf
         export NXF_WORK=$(pwd)
 
-    # Set up Nextflow
     - name: Install Nextflow
       uses: nf-core/setup-nextflow@v2
       with:

.github/workflows/create-lint-wf.yml

@@ -27,14 +27,12 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   MakeTestWorkflow:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         NXF_VER:

.github/workflows/create-test-lint-wf-template.yml

@@ -51,6 +51,7 @@ jobs:
     needs: prepare-matrix
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }}

.github/workflows/create-test-wf.yml

@@ -27,15 +27,13 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-env:
-  NXF_ANSI_LOG: false
-
 jobs:
   RunTestWorkflow:
     # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     env:
       NXF_ANSI_LOG: false
+
     strategy:
       matrix:
         NXF_VER:

.gitpod.yml

@@ -9,11 +9,4 @@ tasks:
 
 vscode:
   extensions:
-    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
-    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
-    - nextflow.nextflow # Nextflow syntax highlighting
-    - oderwat.indent-rainbow # Highlight indentation level
-    - streetsidesoftware.code-spell-checker # Spelling checker for source code
-    - charliermarsh.ruff # Code linter Ruff
+    - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.1
+    rev: v0.8.2
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "python.testing.pytestEnabled": true,
+    "python.testing.unittestEnabled": false,
+    "python.testing.nosetestsEnabled": false,
+    "python.testing.pytestArgs": ["tests", "-v", "--tb=short"],
+    "python.testing.autoTestDiscoverOnSaveEnabled": true,
+    "python.terminal.activateEnvInCurrentTerminal": true,
+    "python.terminal.shellIntegration.enabled": true
+}

CHANGELOG.md

@@ -12,15 +12,21 @@
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
 - Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
 - Move `includeConfig 'conf/modules.config'` next to `includeConfig 'conf/base.config'` to not overwrite tests profiles configurations ([#3301](https://github.com/nf-core/tools/pull/3301))
+- Use `params.monochrome_logs` in the template and update nf-core components ([#3310](https://github.com/nf-core/tools/pull/3310))
+- Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302))
+- Add `manifest.contributors` to `nextflow.config` ([#3311](https://github.com/nf-core/tools/pull/3311))
 
 ### Download
 
 - First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
+- Further steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Enable limited support for `oras://` container paths (_only absolute URIs, no flexible registries like with Docker_) and prevent unnecessary image downloads for Seqera Container modules with `reconcile_seqera_container_uris()` ([#3293](https://github.com/nf-core/tools/pull/3293)).
 - Update dawidd6/action-download-artifact action to v7 ([#3306](https://github.com/nf-core/tools/pull/3306))
 
 ### Linting
 
-- General: Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+- allow mixed `str` and `dict` entries in lint config ([#3228](https://github.com/nf-core/tools/pull/3228))
+- fix meta_yml linting test failing due to module.process_name always being "" ([#3317](https://github.com/nf-core/tools/pull/3317))
+- fix module section regex matching wrong things ([#3321](https://github.com/nf-core/tools/pull/3321))
 
 ### Modules
 
@@ -29,6 +35,7 @@
 ### Subworkflows
 
 - Add `nf-core subworkflows patch` command ([#2861](https://github.com/nf-core/tools/pull/2861))
+- Improve subworkflow nf-test migration warning ([#3298](https://github.com/nf-core/tools/pull/3298))
 
 ### General
 
@@ -42,6 +49,7 @@
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
+- fix headers in api docs ([#3323](https://github.com/nf-core/tools/pull/3323))
 - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
 - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
@@ -50,6 +58,13 @@
 - Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283))
 - Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 ([#3299](https://github.com/nf-core/tools/pull/3299))
+- Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309))
+- Run pre-commit when testing linting the template pipeline ([#3280](https://github.com/nf-core/tools/pull/3280))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 ([#3325](https://github.com/nf-core/tools/pull/3325))
+- Make CLI prompt less nf-core specific ([#3326](https://github.com/nf-core/tools/pull/3326))
+- Update gitpod vscode extensions to use nf-core extension pack ([#3327](https://github.com/nf-core/tools/pull/3327))
+- Remove toList() channel operation from inside onComplete block ([#3304](https://github.com/nf-core/tools/pull/3304))
+- build: Setup VS Code tests ([#3292](https://github.com/nf-core/tools/pull/3292))
 - Update dependency textual-dev to v1.7.0 ([#3308](https://github.com/nf-core/tools/pull/3308))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:2a6386ad2db20e7f55073f69a98d6da2cf9f168e05e7487d2670baeb9b7601c5
+FROM python:3.12-slim@sha256:2b0079146a74e23bf4ae8f6a28e1b484c6292f6fb904cbb51825b4a19812fcd8
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

docs/api/_src/api/pipelines/bump_version.md

@@ -1,4 +1,4 @@
-# nf_core.bump_version
+# nf_core.pipelines.bump_version
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.bump_version