Merge branch 'dev' into fix-component-update-script

Author: ningyuxin1999

.editorconfig

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.5
+    rev: v0.9.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -11,13 +11,26 @@ repos:
       - id: prettier
         additional_dependencies:
           - [email protected]
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.2.0"
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
-
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*\.snap$|
+              nf_core/pipeline-template/subworkflows/.*|
+              nf_core/pipeline-template/modules/.*|
+              tests/pipelines/__snapshots__/.*
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*\.snap$|
+              nf_core/pipeline-template/subworkflows/.*|
+              nf_core/pipeline-template/modules/.*|
+              tests/pipelines/__snapshots__/.*
+          )$
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v1.15.0"
     hooks:

.pre-commit-config.yaml

@@ -12,4 +12,3 @@ tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
 *.pyc
-

.prettierignore

@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

.prettierrc.yml

@@ -16,6 +16,8 @@
 
 ### Modules
 
+- increase meta index for multiple input channels ([#3463](https://github.com/nf-core/tools/pull/3463))
+
 ### Subworkflows
 
 ### General
@@ -31,6 +33,9 @@
 - 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))
+- Cleanup: Removed Redundant if Condition ([#3468](https://github.com/nf-core/tools/pull/3468))
+- chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 

CHANGELOG.md

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:34656cd90456349040784165b9decccbcee4de66f3ead0a1168ba893455afd1e
+FROM python:3.12-slim@sha256:aaa3f8cb64dd64e5f8cb6e58346bdcfa410a108324b0f28f1a7cc5964355b211
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

Dockerfile

@@ -33,7 +33,8 @@ process {{ component_name_underscore|upper }} {
     {%- 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 }}
+    {% set meta_index = loop.index|string if not loop.first else '' %}
+    {{ 'tuple val(meta' + meta_index + '), path(' + input_name + ')' if has_meta else 'path ' + input_name }}
     {%- endfor %}
     {%- else -%}
     {% if not_empty_template -%}

nf_core/assets/logo/placeholder_logo.svg

@@ -29,7 +29,7 @@ input:
   {% if inputs -%}
   {% for input_name, ontologies in inputs.items() -%}
   {% if has_meta %}
-  - - meta:
+  - - meta{{ loop.index|string if not loop.first else '' }}:
         type: map
         description: |
           Groovy Map containing sample information

nf_core/module-template/main.nf

@@ -18,8 +18,6 @@ concurrency:
 jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

nf_core/module-template/meta.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295 # v9
         with:
           workflow: linting.yml
           workflow_conclusion: completed

nf_core/pipeline-template/.editorconfig

@@ -5,9 +5,23 @@ repos:
       - id: prettier
         additional_dependencies:
           - [email protected]
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.2.0"
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              modules/nf-core/.*|
+              subworkflows/nf-core/.*|
+              .*\.snap$
+          )$

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

@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

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

@@ -303,4 +303,4 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-{% endif %}
+{%- endif %}