Merge branch 'dev' into fix-linting-error

.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:

.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

@@ -34,6 +34,7 @@
 ### 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
 
@@ -57,6 +58,7 @@
 - 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))
 
 ## [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/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/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",

nf_core/pipelines/create/create.py

@@ -57,7 +57,7 @@ def __init__(
         template_config: Optional[Union[CreateConfig, str, Path]] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
-        default_branch: Optional[str] = None,
+        default_branch: str = "main",
         is_interactive: bool = False,
     ) -> None:
         if isinstance(template_config, CreateConfig):
@@ -87,8 +87,17 @@ def __init__(
         # Read features yaml file
         self.template_features_yml = load_features_yaml()
 
+        # Set fields used by the class methods
+        self.no_git = no_git
+        self.default_branch = default_branch
+        self.is_interactive = is_interactive
+
         if self.config.outdir is None:
             self.config.outdir = str(Path.cwd())
+
+        # Get the default branch name from the Git configuration
+        self.get_default_branch()
+
         self.jinja_params, self.skip_areas = self.obtain_jinja_params_dict(
             self.config.skip_features or [], str(self.config.outdir)
         )
@@ -107,11 +116,6 @@ def __init__(
 
         # Set convenience variables
         self.name = self.config.name
-
-        # Set fields used by the class methods
-        self.no_git = no_git
-        self.default_branch = default_branch
-        self.is_interactive = is_interactive
         self.force = self.config.force
 
         if self.config.outdir == ".":
@@ -233,6 +237,7 @@ def obtain_jinja_params_dict(
         jinja_params["name_docker"] = jinja_params["name"].replace(jinja_params["org"], jinja_params["prefix_nodash"])
         jinja_params["logo_light"] = f"{jinja_params['name_noslash']}_logo_light.png"
         jinja_params["logo_dark"] = f"{jinja_params['name_noslash']}_logo_dark.png"
+        jinja_params["default_branch"] = self.default_branch
         if config_yml is not None:
             if (
                 hasattr(config_yml, "lint")
@@ -254,6 +259,7 @@ def obtain_jinja_params_dict(
 
     def init_pipeline(self):
         """Creates the nf-core pipeline."""
+
         # Make the new pipeline
         self.render_template()
 
@@ -421,33 +427,37 @@ def make_pipeline_logo(self):
                 force=bool(self.force),
             )
 
-    def git_init_pipeline(self) -> None:
-        """Initialises the new pipeline as a Git repository and submits first commit.
-
-        Raises:
-            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
-        """
-        default_branch: Optional[str] = self.default_branch
+    def get_default_branch(self) -> None:
+        """Gets the default branch name from the Git configuration."""
         try:
-            default_branch = default_branch or str(git.config.GitConfigParser().get_value("init", "defaultBranch"))
+            self.default_branch = (
+                str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "main"
+            )  # default to main
         except configparser.Error:
             log.debug("Could not read init.defaultBranch")
-        if default_branch in ["dev", "TEMPLATE"]:
+        if self.default_branch in ["dev", "TEMPLATE"]:
             raise UserWarning(
-                f"Your Git defaultBranch '{default_branch}' is incompatible with nf-core.\n"
+                f"Your Git defaultBranch '{self.default_branch}' is incompatible with nf-core.\n"
                 "'dev' and 'TEMPLATE' can not be used as default branch name.\n"
                 "Set the default branch name with "
                 "[white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
                 "Or set the default_branch parameter in this class.\n"
                 "Pipeline git repository will not be initialised."
             )
 
+    def git_init_pipeline(self) -> None:
+        """Initialises the new pipeline as a Git repository and submits first commit.
+
+        Raises:
+            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
+        """
+
         log.info("Initialising local pipeline git repository")
         repo = git.Repo.init(self.outdir)
         repo.git.add(A=True)
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
-        if default_branch:
-            repo.active_branch.rename(default_branch)
+        if self.default_branch:
+            repo.active_branch.rename(self.default_branch)
         try:
             repo.git.branch("TEMPLATE")
             repo.git.branch("dev")

nf_core/pipelines/download.py

@@ -1744,7 +1744,7 @@ def tidy_tags_and_branches(self):
                 for tag in tags_to_remove:
                     self.repo.delete_tag(tag)
 
-                # switch to a revision that should be kept, because deleting heads fails, if they are checked out (e.g. "master")
+                # switch to a revision that should be kept, because deleting heads fails, if they are checked out (e.g. "main")
                 self.checkout(self.revision[0])
 
                 # delete unwanted heads/branches from repository

nf_core/pipelines/lint/actions_awsfulltest.py

@@ -42,7 +42,7 @@ def actions_awsfulltest(self) -> Dict[str, List[str]]:
 
         # Check that the action is only turned on for published releases
         try:
-            if wf[True]["pull_request"]["branches"] != ["master"]:
+            if wf[True]["pull_request"]["branches"] != ["main", "master"]:
                 raise AssertionError()
             if wf[True]["pull_request_review"]["types"] != ["submitted"]:
                 raise AssertionError()

nf_core/pipelines/lint/version_consistency.py

@@ -5,7 +5,7 @@ def version_consistency(self):
     """Pipeline and container version number consistency.
 
     .. note:: This test only runs when the ``--release`` flag is set for ``nf-core pipelines lint``,
-              or ``$GITHUB_REF`` is equal to ``master``.
+              or ``$GITHUB_REF`` is equal to ``main``.
 
     This lint fetches the pipeline version number from three possible locations:
 

nf_core/pipelines/schema.py

@@ -517,11 +517,13 @@ def validate_schema_title_description(self, schema=None):
             if "title" not in self.schema:
                 raise AssertionError("Schema missing top-level `title` attribute")
             # Validate that id, title and description match the pipeline manifest
-            id_attr = "https://raw.githubusercontent.com/{}/master/nextflow_schema.json".format(
+            id_attr = "https://raw.githubusercontent.com/{}/main/nextflow_schema.json".format(
                 self.pipeline_manifest["name"].strip("\"'")
             )
-            if self.schema["$id"] != id_attr:
-                raise AssertionError(f"Schema `$id` should be `{id_attr}`\n Found `{self.schema['$id']}`")
+            if self.schema["$id"] not in [id_attr, id_attr.replace("/main/", "/master/")]:
+                raise AssertionError(
+                    f"Schema `$id` should be `{id_attr}` or {id_attr.replace('/main/', '/master/')}. \n Found `{self.schema['$id']}`"
+                )
 
             title_attr = "{} pipeline parameters".format(self.pipeline_manifest["name"].strip("\"'"))
             if self.schema["title"] != title_attr:

nf_core/subworkflows/lint/subworkflow_tests.py

@@ -50,7 +50,7 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent):
             subworkflow.warned.append(
                 (
                     "test_dir_exists",
-                    "nf-test directory is missing",
+                    "Migrate pytest-workflow to nf-test",
                     subworkflow.nftest_testdir,
                 )
             )