Merge branch 'dev' into remove_tags.yml

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4
+    rev: v0.4.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -9,24 +9,36 @@
 ### Linting
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
+- Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
 
 ### Download
 
 ### Components
 
+- The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005))
+
 ### General
 
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.4 ([#2974](https://github.com/nf-core/tools/pull/2974))
 - Update gitpod/workspace-base Docker digest to 92dd1bc ([#2982](https://github.com/nf-core/tools/pull/2982))
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
+- return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
+- Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
+- README - absolute image paths ([#3013](https://github.com/nf-core/tools/pull/3013))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.7 ([#3015](https://github.com/nf-core/tools/pull/3015))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.8 ([#3017](https://github.com/nf-core/tools/pull/3017))
+- Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
+- Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
 ### Template
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
+- Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
 
 ### General
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:afc139a0a640942491ec481ad8dda10f2c5b753f5c969393b12480155fe15a63
+FROM python:3.12-slim@sha256:2fba8e70a87bcc9f6edd20dda0a1d4adb32046d2acbca7361bc61da5a106a914
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

README.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-tools_logo_dark.png">
-    <img alt="nf-core/tools" src="docs/images/nfcore-tools_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_dark.png">
+    <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/master/docs/images/nfcore-tools_logo_light.png">
   </picture>
 </h1><!-- omit in toc -->
 

nf_core/components/create.py

@@ -155,6 +155,10 @@ def create(self):
             if self.component_type == "modules":
                 self._get_module_structure_components()
 
+        # Add a valid organization name for nf-test tags
+        not_alphabet = re.compile(r"[^a-zA-Z]")
+        self.org_alphabet = not_alphabet.sub("", self.org)
+
         # Create component template with jinja2
         self._render_template()
         log.info(f"Created component template: '{self.component_name}'")

nf_core/module-template/tests/main.nf.test.j2

@@ -7,7 +7,7 @@ nextflow_process {
     process "{{ component_name_underscore|upper }}"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_{{ org_alphabet }}"
     {%- if subtool %}
     tag "{{ component }}"
     {%- endif %}

nf_core/modules/lint/main_nf.py

@@ -367,14 +367,14 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             # response = _bioconda_package(bp)
             response = nf_core.utils.anaconda_package(bp)
         except LookupError:
-            self.warned.append(("bioconda_version", "Conda version not specified correctly", self.main_nf))
+            self.warned.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf))
         except ValueError:
-            self.failed.append(("bioconda_version", "Conda version not specified correctly", self.main_nf))
+            self.failed.append(("bioconda_version", f"Conda version not specified correctly: {bp}", self.main_nf))
         else:
             # Check that required version is available at all
             if bioconda_version not in response.get("versions"):
                 self.failed.append(
-                    ("bioconda_version", f"Conda package had unknown version: `{bioconda_version}`", self.main_nf)
+                    ("bioconda_version", f"Conda package {bp} had unknown version: `{bioconda_version}`", self.main_nf)
                 )
                 continue  # No need to test for latest version, continue linting
             # Check version is latest available

nf_core/modules/lint/module_tests.py

@@ -4,6 +4,7 @@
 
 import json
 import logging
+import re
 from pathlib import Path
 
 import yaml
@@ -169,7 +170,10 @@ def module_tests(_, module: NFCoreComponent):
                     )
             # Verify that tags are correct.
             main_nf_tags = module._get_main_nf_tags(module.nftest_main_nf)
-            required_tags = ["modules", "modules_nfcore", module.component_name]
+            not_alphabet = re.compile(r"[^a-zA-Z]")
+            org_alp = not_alphabet.sub("", module.org)
+            org_alphabet = org_alp if org_alp != "" else "nfcore"
+            required_tags = ["modules", f"modules_{org_alphabet}", module.component_name]
             if module.component_name.count("/") == 1:
                 required_tags.append(module.component_name.split("/")[0])
             chained_components_tags = module._get_included_components_in_chained_tests(module.nftest_main_nf)

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

@@ -41,10 +41,16 @@ jobs:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yaml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core lint
         env:

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

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

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

@@ -0,0 +1,42 @@
+name: nf-core template version comment
+# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
+# It posts a comment to the PR, even if it comes from a fork.
+
+on: pull_request_target
+
+jobs:
+  template_version:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Read template version from .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
+      - name: Install nf-core
+        run: |
+          python -m pip install --upgrade pip
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+
+      - name: Check nf-core outdated
+        id: nf_core_outdated
+        run: pip list --outdated | grep nf-core
+
+      - name: Post nf-core template version comment
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        if: |
+          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+        with:
+          repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
+          allow-repeats: false
+          message: |
+            ## :warning: Newer version of the nf-core template is available.
+
+            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            Please update your pipeline to the latest version.
+
+            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).

nf_core/pipeline-template/nextflow.config

@@ -187,13 +187,14 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
+apptainer.registry    = 'quay.io'
+docker.registry       = 'quay.io'
+podman.registry       = 'quay.io'
+singularity.registry  = 'quay.io'
+charliecloud.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {

nf_core/pipelines/create/__init__.py

@@ -5,6 +5,7 @@
 from textual.app import App
 from textual.widgets import Button
 
+from nf_core.pipelines.create import utils
 from nf_core.pipelines.create.basicdetails import BasicDetails
 from nf_core.pipelines.create.custompipeline import CustomPipeline
 from nf_core.pipelines.create.finaldetails import FinalDetails
@@ -14,15 +15,10 @@
 from nf_core.pipelines.create.loggingscreen import LoggingScreen
 from nf_core.pipelines.create.nfcorepipeline import NfcorePipeline
 from nf_core.pipelines.create.pipelinetype import ChoosePipelineType
-from nf_core.pipelines.create.utils import (
-    CreateConfig,
-    CustomLogHandler,
-    LoggingConsole,
-)
 from nf_core.pipelines.create.welcome import WelcomeScreen
 
-log_handler = CustomLogHandler(
-    console=LoggingConsole(classes="log_console"),
+log_handler = utils.CustomLogHandler(
+    console=utils.LoggingConsole(classes="log_console"),
     rich_tracebacks=True,
     show_time=False,
     show_path=False,
@@ -36,7 +32,7 @@
 log_handler.setLevel("INFO")
 
 
-class PipelineCreateApp(App[CreateConfig]):
+class PipelineCreateApp(App[utils.CreateConfig]):
     """A Textual app to manage stopwatches."""
 
     CSS_PATH = "create.tcss"
@@ -60,10 +56,10 @@ class PipelineCreateApp(App[CreateConfig]):
     }
 
     # Initialise config as empty
-    TEMPLATE_CONFIG = CreateConfig()
+    TEMPLATE_CONFIG = utils.CreateConfig()
 
     # Initialise pipeline type
-    PIPELINE_TYPE = None
+    NFCORE_PIPELINE = True
 
     # Log handler
     LOG_HANDLER = log_handler
@@ -78,10 +74,12 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
         if event.button.id == "start":
             self.push_screen("choose_type")
         elif event.button.id == "type_nfcore":
-            self.PIPELINE_TYPE = "nfcore"
+            self.NFCORE_PIPELINE = True
+            utils.NFCORE_PIPELINE_GLOBAL = True
             self.push_screen("basic_details")
         elif event.button.id == "type_custom":
-            self.PIPELINE_TYPE = "custom"
+            self.NFCORE_PIPELINE = False
+            utils.NFCORE_PIPELINE_GLOBAL = False
             self.push_screen("basic_details")
         elif event.button.id == "continue":
             self.push_screen("final_details")

nf_core/pipelines/create/basicdetails.py

@@ -39,7 +39,7 @@ def compose(self) -> ComposeResult:
                 "GitHub organisation",
                 "nf-core",
                 classes="column",
-                disabled=self.parent.PIPELINE_TYPE == "nfcore",
+                disabled=self.parent.NFCORE_PIPELINE,
             )
             yield TextInput(
                 "name",
@@ -85,7 +85,7 @@ def on_screen_resume(self):
         add_hide_class(self.parent, "exist_warn")
         for text_input in self.query("TextInput"):
             if text_input.field_id == "org":
-                text_input.disabled = self.parent.PIPELINE_TYPE == "nfcore"
+                text_input.disabled = self.parent.NFCORE_PIPELINE
 
     @on(Button.Pressed)
     def on_button_pressed(self, event: Button.Pressed) -> None:
@@ -102,9 +102,9 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
         try:
             self.parent.TEMPLATE_CONFIG = CreateConfig(**config)
             if event.button.id == "next":
-                if self.parent.PIPELINE_TYPE == "nfcore":
+                if self.parent.NFCORE_PIPELINE:
                     self.parent.push_screen("type_nfcore")
-                elif self.parent.PIPELINE_TYPE == "custom":
+                else:
                     self.parent.push_screen("type_custom")
         except ValueError:
             pass

nf_core/pipelines/create/utils.py

@@ -1,9 +1,11 @@
 import re
+from contextlib import contextmanager
+from contextvars import ContextVar
 from logging import LogRecord
 from pathlib import Path
-from typing import Optional, Union
+from typing import Any, Dict, Iterator, Optional, Union
 
-from pydantic import BaseModel, ConfigDict, ValidationError, field_validator
+from pydantic import BaseModel, ConfigDict, ValidationError, ValidationInfo, field_validator
 from rich.logging import RichHandler
 from textual import on
 from textual._context import active_app
@@ -14,6 +16,22 @@
 from textual.widget import Widget
 from textual.widgets import Button, Input, Markdown, RichLog, Static, Switch
 
+# Use ContextVar to define a context on the model initialization
+_init_context_var: ContextVar = ContextVar("_init_context_var", default={})
+
+
+@contextmanager
+def init_context(value: Dict[str, Any]) -> Iterator[None]:
+    token = _init_context_var.set(value)
+    try:
+        yield
+    finally:
+        _init_context_var.reset(token)
+
+
+# Define a global variable to store the pipeline type
+NFCORE_PIPELINE_GLOBAL: bool = True
+
 
 class CreateConfig(BaseModel):
     """Pydantic model for the nf-core create config."""
@@ -30,12 +48,25 @@ class CreateConfig(BaseModel):
 
     model_config = ConfigDict(extra="allow")
 
+    def __init__(self, /, **data: Any) -> None:
+        """Custom init method to allow using a context on the model initialization."""
+        self.__pydantic_validator__.validate_python(
+            data,
+            self_instance=self,
+            context=_init_context_var.get(),
+        )
+
     @field_validator("name")
     @classmethod
-    def name_nospecialchars(cls, v: str) -> str:
+    def name_nospecialchars(cls, v: str, info: ValidationInfo) -> str:
         """Check that the pipeline name is simple."""
-        if not re.match(r"^[a-z]+$", v):
-            raise ValueError("Must be lowercase without punctuation.")
+        context = info.context
+        if context and context["is_nfcore"]:
+            if not re.match(r"^[a-z]+$", v):
+                raise ValueError("Must be lowercase without punctuation.")
+        else:
+            if not re.match(r"^[a-zA-Z-_]+$", v):
+                raise ValueError("Must not contain special characters. Only '-' or '_' are allowed.")
         return v
 
     @field_validator("org", "description", "author", "version", "outdir")
@@ -117,8 +148,9 @@ def validate(self, value: str) -> ValidationResult:
 
         If it fails, return the error messages."""
         try:
-            CreateConfig(**{f"{self.key}": value})
-            return self.success()
+            with init_context({"is_nfcore": NFCORE_PIPELINE_GLOBAL}):
+                CreateConfig(**{f"{self.key}": value})
+                return self.success()
         except ValidationError as e:
             return self.failure(", ".join([err["msg"] for err in e.errors()]))
 

nf_core/subworkflow-template/tests/main.nf.test.j2

@@ -7,7 +7,7 @@ nextflow_workflow {
     workflow "{{ component_name_underscore|upper }}"
 
     tag "subworkflows"
-    tag "subworkflows_nfcore"
+    tag "subworkflows_{{ org_alphabet }}"
     tag "subworkflows/{{ component_name }}"
     // TODO nf-core: Add tags for all modules used within this subworkflow. Example:
     tag "samtools"