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

.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

docs/api/_src/api/pipelines/create.md

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

docs/api/_src/api/pipelines/download.md

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

docs/api/_src/api/pipelines/launch.md

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

docs/api/_src/api/pipelines/lint.md

@@ -1,4 +1,4 @@
-# nf_core.lint
+# nf_core.pipelines.lint
 
 :::{seealso}
 See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.

docs/api/_src/api/pipelines/list.md

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

docs/api/_src/api/pipelines/params-file.md

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

docs/api/_src/api/pipelines/schema.md

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

docs/api/_src/api/pipelines/sync.md

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

docs/api/_src/api/pipelines/utils.md

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

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/lint/__init__.py

@@ -22,7 +22,7 @@
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.pipelines.lint_utils import console
-from nf_core.utils import LintConfigType
+from nf_core.utils import NFCoreYamlLintConfig
 from nf_core.utils import plural_s as _s
 
 log = logging.getLogger(__name__)
@@ -80,7 +80,7 @@ def __init__(
         self.failed: List[LintResult] = []
         self.all_local_components: List[NFCoreComponent] = []
 
-        self.lint_config: Optional[LintConfigType] = None
+        self.lint_config: Optional[NFCoreYamlLintConfig] = None
         self.modules_json: Optional[ModulesJson] = None
 
         if self.component_type == "modules":

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/gitpod/gitpod.Dockerfile

@@ -2,7 +2,7 @@
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base@sha256:2cc134fe5bd7d8fdbe44cab294925d4bc6d2d178d94624f4c376584a22d1f7b6
+FROM gitpod/workspace-base@sha256:12853f7c901eb2b677a549cb112c85f9679d18feb30093bcc63aa252540ecad9
 
 USER root
 

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

@@ -1,4 +1,4 @@
-# {{ name }}: Contributing Guidelines
+# `{{ name }}`: Contributing Guidelines
 
 Hi there!
 Many thanks for taking an interest in improving {{ name }}.
@@ -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).
-- A PR should be made on `master` from patch to directly this particular bug.
+- Open a pull-request from `patch` to `main`/`master` with the changes.
 
 {% if is_nfcore -%}
 
@@ -78,13 +78,13 @@ For further information/help, please consult the [{{ name }} documentation](http
 
 ## Pipeline contribution conventions
 
-To make the {{ name }} code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `{{ name }}` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
 If you wish to contribute a new step, please use the following coding standards:
 
-1. Define the corresponding input channel into your new process from the expected previous process channel
+1. Define the corresponding input channel into your new process from the expected previous process channel.
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
@@ -99,7 +99,7 @@ If you wish to contribute a new step, please use the following coding standards:
 
 ### Default values
 
-Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
+Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
 Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
 

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: