Merge branch 'dev' into remove-channel-operations-from-oncomplete

.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

CHANGELOG.md

@@ -25,6 +25,8 @@
 ### Linting
 
 - 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
 
@@ -33,6 +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
 
@@ -56,6 +59,9 @@
 - 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))
 
 ## [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="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

nf_core/__main__.py

@@ -288,7 +288,7 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
 @click.option(
     "--release",
     is_flag=True,
-    default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master"
+    default=Path(os.environ.get("GITHUB_REF", "").strip(" '\"")).parent.name in ["master", "main"]
     and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/")
     and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools",
     help="Execute additional checks for release-ready workflows.",
@@ -2240,7 +2240,7 @@ def command_download(
 @click.option(
     "--release",
     is_flag=True,
-    default=os.path.basename(os.path.dirname(os.environ.get("GITHUB_REF", "").strip(" '\""))) == "master"
+    default=Path(os.environ.get("GITHUB_REF", "").strip(" '\"")).parent.name in ["master", "main"]
     and os.environ.get("GITHUB_REPOSITORY", "").startswith("nf-core/")
     and not os.environ.get("GITHUB_REPOSITORY", "") == "nf-core/tools",
     help="Execute additional checks for release-ready workflows.",

nf_core/components/components_utils.py

@@ -43,10 +43,10 @@ def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[P
     if not repo_type and use_prompt:
         log.warning("'repository_type' not defined in %s", config_fn.name)
         repo_type = questionary.select(
-            "Is this repository an nf-core pipeline or a fork of nf-core/modules?",
+            "Is this repository a pipeline or a modules repository?",
             choices=[
                 {"name": "Pipeline", "value": "pipeline"},
-                {"name": "nf-core/modules", "value": "modules"},
+                {"name": "Modules repository", "value": "modules"},
             ],
             style=nf_core.utils.nfcore_question_style,
         ).unsafe_ask()

nf_core/components/nfcore_component.py

@@ -62,7 +62,6 @@ def __init__(
             # Initialize the important files
             self.main_nf: Path = Path(self.component_dir, "main.nf")
             self.meta_yml: Optional[Path] = Path(self.component_dir, "meta.yml")
-            self.process_name = ""
             self.environment_yml: Optional[Path] = Path(self.component_dir, "environment.yml")
 
             component_list = self.component_name.split("/")
@@ -96,6 +95,8 @@ def __init__(
             self.test_yml = None
             self.test_main_nf = None
 
+        self.process_name: str = self._get_process_name()
+
     def __repr__(self) -> str:
         return f"<NFCoreComponent {self.component_name} {self.component_dir} {self.repo_url}>"
 
@@ -169,6 +170,13 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
                         included_components.append(component)
         return included_components
 
+    def _get_process_name(self):
+        with open(self.main_nf) as fh:
+            for line in fh:
+                if re.search(r"^\s*process\s*\w*\s*{", line):
+                    return re.search(r"^\s*process\s*(\w*)\s*{.*", line).group(1) or ""
+        return ""
+
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
         inputs: Any = []  # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]'

nf_core/modules/lint/main_nf.py

@@ -96,19 +96,19 @@ def main_nf(
     for line in iter_lines:
         if re.search(r"^\s*process\s*\w*\s*{", line) and state == "module":
             state = "process"
-        if re.search(r"input\s*:", line) and state in ["process"]:
+        if re.search(r"^\s*input\s*:", line) and state in ["process"]:
             state = "input"
             continue
-        if re.search(r"output\s*:", line) and state in ["input", "process"]:
+        if re.search(r"^\s*output\s*:", line) and state in ["input", "process"]:
             state = "output"
             continue
-        if re.search(r"when\s*:", line) and state in ["input", "output", "process"]:
+        if re.search(r"^\s*when\s*:", line) and state in ["input", "output", "process"]:
             state = "when"
             continue
-        if re.search(r"script\s*:", line) and state in ["input", "output", "when", "process"]:
+        if re.search(r"^\s*script\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "script"
             continue
-        if re.search(r"shell\s*:", line) and state in ["input", "output", "when", "process"]:
+        if re.search(r"^\s*shell\s*:", line) and state in ["input", "output", "when", "process"]:
             state = "shell"
             continue
 
@@ -256,7 +256,6 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     bioconda_packages = []
 
     # Process name should be all capital letters
-    self.process_name = lines[0].split()[1]
     if all(x.upper() for x in self.process_name):
         self.passed.append(("process_capitals", "Process name is in capital letters", self.main_nf))
     else:

nf_core/pipeline-template/.github/CONTRIBUTING.md

@@ -64,9 +64,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`.
 - Fix the bug, and bump version (X.Y.Z+1).
-- Open a pull-request from `patch` to `master` with the changes.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 {% if is_nfcore -%}
 

nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/tree/{{ default_branch }}/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/{{ name }}/tree/{{ default_branch }}/.github/CONTRIBUTING.md)
       {%- if is_nfcore %}
 - [ ] If necessary, also make a PR on the {{ name }} _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
       {%- endif %}

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -1,11 +1,12 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on PRs opened against the master branch.
+# This workflow is triggered on PRs opened against the main/master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
   pull_request:
     branches:
+      - main
       - master
   workflow_dispatch:
   pull_request_review:

nf_core/pipeline-template/.github/workflows/branch.yml

@@ -1,15 +1,17 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to `main`/`master` branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches:
+      - main
+      - master
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == '{{ name }}'
         run: |
@@ -22,7 +24,7 @@ jobs:
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +34,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
+            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

nf_core/pipeline-template/.github/workflows/download_pipeline.yml

@@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download'
 
 # Run the workflow when:
 #  - dispatched manually
-#  - when a PR is opened or reopened to master branch
+#  - when a PR is opened or reopened to main/master branch
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
@@ -17,9 +17,11 @@ on:
       - edited
       - synchronize
     branches:
+      - main
       - master
   pull_request_target:
     branches:
+      - main
       - master
 
 env:

nf_core/pipeline-template/.gitpod.yml

@@ -6,13 +6,6 @@ tasks:
       nextflow self-update
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:
     #{%- if code_linters -%}
-    - 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{% endif %}
-    - 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

nf_core/pipeline-template/assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/{{ name }}/master/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/{{ name }}/{{ default_branch }}/assets/schema_input.json",
     "title": "{{ name }} pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

nf_core/pipeline-template/nextflow.config

@@ -291,6 +291,7 @@ manifest {
     homePage        = 'https://github.com/{{ name }}'
     description     = """{{ description }}"""
     mainScript      = 'main.nf'
+    defaultBranch   = '{{ default_branch }}'
     nextflowVersion = '!>=24.04.2'
     version         = '{{ version }}'
     doi             = ''

nf_core/pipeline-template/nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/{{ name }}/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/{{ name }}/{{ default_branch }}/nextflow_schema.json",
     "title": "{{ name }} pipeline parameters",
     "description": "{{ description }}",
     "type": "object",