Merge branch 'dev' into renovate/editorconfig-checker-editorconfig-checker.python-3.x

Author: mashehu

.github/workflows/pytest.yml

@@ -75,8 +75,8 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    # run on self-hosted runners for test_components.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
-    runs-on: ${{ matrix.test == 'test_components.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
+    # run on self-hosted runners for test_components_generate_snapshot.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ matrix.test == 'components/test_components_generate_snapshot.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.9.5
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -10,7 +10,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.3.3
+          - prettier@3.5.0
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "3.2.0"
@@ -19,7 +19,7 @@ repos:
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.14.1"
+    rev: "v1.15.0"
     hooks:
       - id: mypy
         additional_dependencies:

CHANGELOG.md

@@ -5,10 +5,14 @@
 ### Template
 
 - Remove the on `pull_request_target` trigger and `pull_request` types from the download test. Also drop `push` triggers on other CI tests. ([#3399](https://github.com/nf-core/tools/pull/3399))
+- Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396))
 
 ### Linting
 
 - Add linting for ifEmpty(null) ([#3411](https://github.com/nf-core/tools/pull/3411))
+- Fix arbitrarily nested params schema linting ([#3443](https://github.com/nf-core/tools/pull/3443))
+- fix: linting with comments after the input directive ([#3458](https://github.com/nf-core/tools/pull/3458))
+- EDAM ontology fixes ([#3460](https://github.com/nf-core/tools/pull/3460))
 
 ### Modules
 
@@ -21,6 +25,12 @@
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
 - format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
 - chore(deps): update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.2.0 ([#3446](https://github.com/nf-core/tools/pull/3446))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
+- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
+- Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
+- chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
+- Remove Twitter from README ([#3454](https://github.com/nf-core/tools/pull/3454))
+- docs: fix contributing link in the main README ([#3459](https://github.com/nf-core/tools/pull/3459))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 
@@ -73,7 +83,7 @@
 - Use outputs instead of the environment to pass around values between steps in the Download Test Action ([#3351](https://github.com/nf-core/tools/pull/3351))
 - Fix pre commit template ([#3358](https://github.com/nf-core/tools/pull/3358))
 - Set LICENSE copyright to nf-core community ([#3366](https://github.com/nf-core/tools/pull/3366))
-- fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
+- Fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
 
 ### Linting
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:69ce3aed05675d284bee807e7c45e560e98db21fb1e4c670252b4ee0f2496b6d
+FROM python:3.12-slim@sha256:34656cd90456349040784165b9decccbcee4de66f3ead0a1168ba893455afd1e
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

README.md

@@ -61,7 +61,7 @@ pip install --upgrade -r requirements-dev.txt -e .
 
 ## Contributions and Support
 
-If you would like to contribute to this package, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this package, please see the [contributing guidelines](CONTRIBUTING.md).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#tools` channel](https://nfcore.slack.com/channels/tools) (you can join with [this invite](https://nf-co.re/join/slack)).
 

nf_core/components/components_utils.py

@@ -1,7 +1,7 @@
 import logging
 import re
 from pathlib import Path
-from typing import TYPE_CHECKING, List, Optional, Tuple, Union
+from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
 
 import questionary
 import requests
@@ -165,9 +165,9 @@ def get_components_to_install(subworkflow_dir: Union[str, Path]) -> Tuple[List[s
     return modules, subworkflows
 
 
-def get_biotools_id(tool_name) -> str:
+def get_biotools_response(tool_name: str) -> Optional[Dict]:
     """
-    Try to find a bio.tools ID for 'tool'
+    Try to get bio.tools information for 'tool'
     """
     url = f"https://bio.tools/api/t/?q={tool_name}&format=json"
     try:
@@ -176,16 +176,74 @@ def get_biotools_id(tool_name) -> str:
         response.raise_for_status()  # Raise an error for bad status codes
         # Parse the JSON response
         data = response.json()
+        log.info(f"Found bio.tools information for '{tool_name}'")
+        return data
 
-        # Iterate through the tools in the response to find the tool name
-        for tool in data["list"]:
-            if tool["name"].lower() == tool_name:
-                return tool["biotoolsCURIE"]
+    except requests.exceptions.RequestException as e:
+        log.warning(f"Could not find bio.tools information for '{tool_name}': {e}")
+        return None
 
-        # If the tool name was not found in the response
-        log.warning(f"Could not find a bio.tools ID for '{tool_name}'")
-        return ""
 
-    except requests.exceptions.RequestException as e:
-        log.warning(f"Could not find a bio.tools ID for '{tool_name}': {e}")
-        return ""
+def get_biotools_id(data: dict, tool_name: str) -> str:
+    """
+    Try to find a bio.tools ID for 'tool'
+    """
+    # Iterate through the tools in the response to find the tool name
+    for tool in data["list"]:
+        if tool["name"].lower() == tool_name:
+            log.info(f"Found bio.tools ID: '{tool['biotoolsCURIE']}'")
+            return tool["biotoolsCURIE"]
+
+    # If the tool name was not found in the response
+    log.warning(f"Could not find a bio.tools ID for '{tool_name}'")
+    return ""
+
+
+DictWithStrAndTuple = Dict[str, Tuple[List[str], List[str], List[str]]]
+
+
+def get_channel_info_from_biotools(
+    data: dict, tool_name: str
+) -> Optional[Tuple[DictWithStrAndTuple, DictWithStrAndTuple]]:
+    """
+    Try to find input and output channels and the respective EDAM ontology terms
+
+    Args:
+        data (dict): The bio.tools API response
+        tool_name (str): The name of the tool
+    """
+    inputs = {}
+    outputs = {}
+
+    def _iterate_input_output(type) -> DictWithStrAndTuple:
+        type_info = {}
+        if type in funct:
+            for element in funct[type]:
+                if "data" in element:
+                    element_name = "_".join(element["data"]["term"].lower().split(" "))
+                    uris = [element["data"]["uri"]]
+                    terms = [element["data"]["term"]]
+                    patterns = []
+                if "format" in element:
+                    for format in element["format"]:
+                        # Append the EDAM URI
+                        uris.append(format["uri"])
+                        # Append the EDAM term, getting the first word in case of complicated strings. i.e. "FASTA format"
+                        patterns.append(format["term"].lower().split(" ")[0])
+                        terms.append(format["term"])
+                    type_info[element_name] = (uris, terms, patterns)
+        return type_info
+
+    # Iterate through the tools in the response to find the tool name
+    for tool in data["list"]:
+        if tool["name"].lower() == tool_name:
+            if "function" in tool:
+                # Parse all tool functions
+                for funct in tool["function"]:
+                    inputs.update(_iterate_input_output("input"))
+                    outputs.update(_iterate_input_output("output"))
+            return inputs, outputs
+
+    # If the tool name was not found in the response
+    log.warning(f"Could not find an EDAM ontology term for '{tool_name}'")
+    return None

nf_core/components/create.py

@@ -21,7 +21,7 @@
 import nf_core
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from nf_core.components.components_utils import get_biotools_id
+from nf_core.components.components_utils import get_biotools_id, get_biotools_response, get_channel_info_from_biotools
 from nf_core.pipelines.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
@@ -151,8 +151,15 @@ def create(self) -> bool:
             if self.component_type == "modules":
                 # Try to find a bioconda package for 'component'
                 self._get_bioconda_tool()
+                name = self.tool_conda_name if self.tool_conda_name else self.component
                 # Try to find a biotools entry for 'component'
-                self.tool_identifier = get_biotools_id(self.component)
+                biotools_data = get_biotools_response(name)
+                if biotools_data:
+                    self.tool_identifier = get_biotools_id(biotools_data, name)
+                    # Obtain EDAM ontologies for inputs and outputs
+                    channel_info = get_channel_info_from_biotools(biotools_data, name)
+                    if channel_info:
+                        self.inputs, self.outputs = channel_info
 
             # Prompt for GitHub username
             self._get_username()
@@ -176,6 +183,8 @@ def create(self) -> bool:
 
         new_files = [str(path) for path in self.file_paths.values()]
 
+        run_prettier_on_file(new_files)
+
         log.info("Created following files:\n  " + "\n  ".join(new_files))
         return True
 

nf_core/components/nfcore_component.py

@@ -206,6 +206,7 @@ def get_inputs_from_main_nf(self) -> None:
             input_data = data.split("input:")[1].split("output:")[0]
             for line in input_data.split("\n"):
                 channel_elements: Any = []
+                line = line.split("//")[0]  # remove any trailing comments
                 regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
                 matches = re.finditer(regex, line)
                 for _, match in enumerate(matches, start=1):

nf_core/module-template/environment.yml

@@ -4,4 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # TODO nf-core: List required Conda package(s).
+  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"

nf_core/module-template/main.nf

@@ -22,9 +22,6 @@ process {{ component_name_underscore|upper }} {
     label '{{ process_label }}'
 
     {% if not_empty_template -%}
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
     conda "${moduleDir}/environment.yml"
@@ -33,6 +30,12 @@ process {{ component_name_underscore|upper }} {
         '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"
 
     input:
+    {%- if inputs %}
+    // TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
+    {%- for input_name, ontologies in inputs.items() %}
+    {{ 'tuple val(meta), path(' + input_name + ')' if has_meta else 'path ' + input_name }}
+    {%- endfor %}
+    {%- else -%}
     {% if not_empty_template -%}
     // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
     //               MUST be provided as an input via a Groovy Map called "meta".
@@ -44,16 +47,22 @@ process {{ component_name_underscore|upper }} {
     {%- else -%}
     {{ 'tuple val(meta), path(input)' if has_meta else 'path input' }}
     {%- endif %}
+    {%- endif %}
 
     output:
+    {%- if outputs %}
+    // TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
+    {%- for output_name, ontologies in outputs.items() %}
+    {{ 'tuple val(meta), path("*.{' + ontologies[2]|join(',') + '}")' if has_meta else 'path ' + output_name }}, emit: {{ output_name }}
+    {%- endfor %}
+    {%- else %}
     {% if not_empty_template -%}
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     {{ 'tuple val(meta), path("*.bam")' if has_meta else 'path "*.bam"' }}, emit: bam
+    // TODO nf-core: List additional required output channels/values here
     {%- else -%}
     {{ 'tuple val(meta), path("*")' if has_meta else 'path "*"' }}, emit: output
     {%- endif %}
-    {% if not_empty_template -%}
-    // TODO nf-core: List additional required output channels/values here
     {%- endif %}
     path "versions.yml"           , emit: versions
 
@@ -78,20 +87,33 @@ process {{ component_name_underscore|upper }} {
     {%- endif %}
     """
     {% if not_empty_template -%}
-    samtools \\
-        sort \\
+    {{ component }} \\
         $args \\
         -@ $task.cpus \\
         {%- if has_meta %}
+        {%- if inputs %}
+        {%- for input_name, ontologies in inputs.items() %}
+        {%- set extensions = ontologies[2] %}
+        {%- for ext in extensions %}
+        -o ${prefix}.{{ ext }} \\
+        {%- endfor %}
+        {%- endfor %}
+        {%- else %}
         -o ${prefix}.bam \\
-        -T $prefix \\
         {%- endif %}
+        {%- endif %}
+        {%- if inputs %}
+        {%- for input_name, ontologies in inputs.items() %}
+        ${{ input_name }} \\
+        {%- endfor %}
+        {%- else %}
         $bam
+        {%- endif %}
     {%- endif %}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        {{ component }}: \$(samtools --version |& sed '1!d ; s/samtools //')
+        {{ component }}: \$({{ component }} --version)
     END_VERSIONS
     """
 
@@ -108,12 +130,21 @@ process {{ component_name_underscore|upper }} {
     {%- endif %}
     """
     {% if not_empty_template -%}
+    {%- if inputs %}
+    {%- for input_name, ontologies in inputs.items() %}
+    {%- set extensions = ontologies[2] %}
+    {%- for ext in extensions %}
+    touch ${prefix}.{{ ext }}
+    {%- endfor %}
+    {%- endfor %}
+    {%- else %}
     touch ${prefix}.bam
     {%- endif %}
+    {%- endif %}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        {{ component }}: \$(samtools --version |& sed '1!d ; s/samtools //')
+        {{ component }}: \$({{ component }} --version)
     END_VERSIONS
     """
 }