Merge branch 'main' into meta-rfc

Author: ewels

.editorconfig

@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js,cff}]
+indent_size = 2

.github/ISSUE_TEMPLATE/new_pipeline.yml

@@ -4,38 +4,37 @@ title: "New pipeline: nf-core/<add provisional pipeline name here>"
 labels: "new-pipeline,proposed"
 projects: nf-core/104
 body:
-
   - type: input
     attributes:
       label: Pipeline title/name
       description: Names should be [lower case, without punctuation, and descriptive](https://nf-co.re/docs/guidelines/pipelines/requirements/workflow_name) (not 'fun' names).
       placeholder: rnaseq
     validations:
-        required: true
+      required: true
 
   - type: input
     attributes:
       label: Keywords
       description: Provide a comma separated list of useful keywords for data type/analysis type/research field of the proposal (e.g. genomics, cancer, variant calling).
       placeholder: genomics, cancer, variant calling
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: What is it about?
       description: Give a short summary of the purpose of the pipeline.
-      placeholder: An RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. 
+      placeholder: An RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: Please provide a schematic diagram of the proposed pipeline
       description: Please use tool names as each 'node'. Drag and drop the image file into the text area to upload.
-      placeholder: ![](https://your.url/image/png)
+      placeholder: "![](https://your.url/image/png)"
     validations:
-        required: true
+      required: true
 
   - type: checkboxes
     attributes:
@@ -66,23 +65,23 @@ body:
       label: Why do we need a new pipeline?
       description: Describe the 'usefuless' or 'novelty' of the pipeline whether analytically or within nf-core.
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: Who would be interested?
       description: Please give possible target audiences of the pipelines.
       placeholder: Researchers working on transcriptomics.
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: What has been done so far
       description: Please describe the current status of the concept or code, or say if you have not stated.
       placeholder: I have started making nf-core modules for tools I would use in the proposed pipeline.
     validations:
-        required: true
+      required: true
 
   - type: input
     attributes:

.github/ISSUE_TEMPLATE/new_rfc.yml

@@ -11,40 +11,39 @@ body:
       label: Summary
       description: Short 2-3 sentence summary of RFC proposal.
     validations:
-        required: true
+      required: true
   - type: input
     attributes:
       label: Champion
       description: "GitHub handle of the proposal's champion (if already found)."
-      placeholder:
-        e.g. @maxulysse
+      placeholder: e.g. @maxulysse
   - type: textarea
     attributes:
       label: Background & Motivation
       description: Provide the context of the proposal, summarising the existing status-quo or issues.
-      placeholder: 
+      placeholder:
     validations:
-        required: true
+      required: true
   - type: textarea
     attributes:
       label: Goals
-      description: Provide a 2-3 bullet point list of the main aims and objectives the outcome RFC aims to achieve 
+      description: Provide a 2-3 bullet point list of the main aims and objectives the outcome RFC aims to achieve
       placeholder: |
         - Goal 1
         - Goal 2
         - Goal 3
     validations:
-        required: true
+      required: true
   - type: textarea
     attributes:
       label: "Non-Goals"
-      description: Provide a 2-3 bullet point list of the main aims and objectives the outcome RFC aims NOT to achieve. 
+      description: Provide a 2-3 bullet point list of the main aims and objectives the outcome RFC aims NOT to achieve.
       placeholder: |
         - Non-goal 1
         - Non-goal 2
         - Non-goal 3
     validations:
-        required: false
+      required: false
   - type: textarea
     attributes:
       label: References
@@ -54,4 +53,4 @@ body:
         - Original GitHub Issue - https://github.com/nf-core/<URL>
         - Prototype - https://github.com/nf-core/<URL>
     validations:
-        required: false
+      required: false

.github/ISSUE_TEMPLATE/new_special_interest_group.yml

@@ -18,36 +18,36 @@ body:
       description: Suggested interest group name. It should be as simple, descriptive and boring as possible.
       placeholder: Animal Genomics
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: What is it about?
       description: Give a one sentence description of the purpose of the special interest group.
     validations:
-        required: true
+      required: true
 
   - type: input
     attributes:
       label: Keywords
       description: Provide a comma separated list of useful keywords for topics related to the proposal (e.g. genomics, cancer, variant calling).
       placeholder: genomics, cancer, variant calling
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: Why do we need a new special interest group?
       description: Describe the 'usefuless' or 'novelty' of the special interest group within nf-core.
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:
       label: Who would be interested?
       description: Please give possible target audiences of the special interest groups.
     validations:
-        required: true
+      required: true
 
   - type: textarea
     attributes:

.github/workflows/pre-commit.yml

@@ -0,0 +1,29 @@
+name: Lint tools code formatting
+on:
+  push:
+  pull_request:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - [email protected]
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.1.2"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120

README.md

@@ -23,13 +23,13 @@ To make a new proposal for a special interest group, please create a new issue i
 
 The curator workflow is as follows:
 
-- [ ]  Once a issue is made, update the 'Project' status to 'proposed' (right hand side bar, under 'new-<TYPE>-proposals')
+- [ ] Once a issue is made, update the 'Project' status to 'proposed' (right hand side bar, under 'new-<TYPE>-proposals')
 - [ ] Facilitate discussion on the the Issue thread, following the guidance [here](https://nf-co.re/docs/checklists/community_governance/core_team#new-pipeline-proposals-and-onboarding).
 - [ ] Acceptance requires a minimum of OKs from:
-    - Two members of the core team.
-    - One member of the core team and one member of the maintainers team.
+  - Two members of the core team.
+  - One member of the core team and one member of the maintainers team.
 - [ ] If a proposal is accepted, update both the label AND status to 'accepted', and when closing select 'Close as completed'
-- [ ] If a proposal is turned down, update both the label AND  status to 'turned-down', and when closing select 'Close as not planned'
+- [ ] If a proposal is turned down, update both the label AND status to 'turned-down', and when closing select 'Close as not planned'
 - [ ] If a proposal is not completed or abandoned after a year, update both the label AND status to 'timed-out', and when closing select 'Close as not planned'
 - [ ] Complete the reemaining new-pipeline onboarding tasks listed [here](https://nf-co.re/docs/checklists/community_governance/core_team#new-pipeline-proposals-and-onboarding)
 
@@ -40,7 +40,7 @@ The curator workflow is as follows:
 - [ ] Once a issue is made, update the 'Project' status to 'proposed' (right hand side bar, under 'new-<TYPE>-proposals')
 - [ ] Facilitate discussion on the the Issue thread, following the guidance [here](https://nf-co.re/blog/2024/special_interest_groups).
 - [ ] Acceptance requires a minimum of OKs from:
-    - Two members of the core team.
+  - Two members of the core team.
 - [ ] If a proposal is accepted, update both the label AND status to 'accepted', and when closing select 'Close as completed'
-- [ ] If a proposal is turned down, update both the label AND  status to 'turned-down', and when closing select 'Close as not planned'
+- [ ] If a proposal is turned down, update both the label AND status to 'turned-down', and when closing select 'Close as not planned'
 - [ ] If a proposal is not completed or abandoned after a year, update both the label AND status to 'timed-out', and when closing select 'Close as not planned'