feat: update nf-core modules and pipeline configs

pipelines/nf-atacseq/.github/.dockstore.yml

@@ -0,0 +1,5 @@
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /pipelines/nf-atacseq/main.nf
+    publish: true

pipelines/nf-atacseq/.github/CONTRIBUTING.md

@@ -0,0 +1,29 @@
+# Contributing to nf-atacseq
+
+## Getting help
+
+For questions, bugs, or feature requests, please open an issue on [GitHub](https://github.com/mcvickerlab/WASP2/issues).
+
+## Development workflow
+
+1. Fork the repository
+2. Create a feature branch from `dev`
+3. Make your changes
+4. Run `nf-core pipelines lint` to verify compliance
+5. Submit a pull request to `dev`
+
+## Code style
+
+- Follow nf-core module conventions for new modules
+- Use `tuple val(meta), path(...)` for all process inputs/outputs
+- Include `stub:` blocks in all processes
+- Add `versions.yml` output to all processes
+- Write `meta.yml` documentation for new modules
+
+## Testing
+
+Run the test profile before submitting changes:
+
+```bash
+nextflow run main.nf -profile test,docker --outdir test_results
+```

pipelines/nf-atacseq/.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: WASP2 Documentation
+    url: https://wasp2.readthedocs.io
+    about: Check the documentation for usage help

pipelines/nf-atacseq/.github/actions/get-shards/action.yml

@@ -0,0 +1,19 @@
+name: Get test shards
+description: Get nf-test shards for parallel execution
+inputs:
+  test-path:
+    description: Path to test files
+    required: false
+    default: tests
+outputs:
+  shards:
+    description: JSON array of test shards
+    value: ${{ steps.get-shards.outputs.shards }}
+runs:
+  using: composite
+  steps:
+    - id: get-shards
+      shell: bash
+      run: |
+        shards=$(find ${{ inputs.test-path }} -name "*.nf.test" | jq -R -s -c 'split("\n") | map(select(. != ""))')
+        echo "shards=$shards" >> $GITHUB_OUTPUT

pipelines/nf-atacseq/.github/actions/nf-test/action.yml

@@ -0,0 +1,15 @@
+name: Run nf-test
+description: Run nf-test for a specific test file
+inputs:
+  test-file:
+    description: Path to the nf-test file
+    required: true
+  profile:
+    description: Nextflow profile to use
+    required: false
+    default: test,docker
+runs:
+  using: composite
+  steps:
+    - shell: bash
+      run: nf-test test ${{ inputs.test-file }} --profile ${{ inputs.profile }}

pipelines/nf-atacseq/.github/workflows/branch.yml

@@ -0,0 +1,13 @@
+name: nf-core branch protection
+on:
+  pull_request_target:
+    branches: [master, main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check PRs
+        if: github.repository == 'mcvickerlab/WASP2'
+        run: |
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == mcvickerlab/WASP2 ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || echo "This PR is not from dev. It will be reviewed manually."

pipelines/nf-atacseq/.github/workflows/linting_comment.yml

@@ -0,0 +1,13 @@
+name: nf-core linting comment
+on:
+  workflow_run:
+    workflows: ["nf-core linting"]
+    types: [completed]
+
+jobs:
+  linting-comment:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Post linting comment
+        run: echo "Linting workflow completed"

pipelines/nf-atacseq/.github/workflows/nf-test.yml

@@ -0,0 +1,40 @@
+name: Run nf-test
+on:
+  pull_request:
+    branches: [dev, master]
+  release:
+    types: [published]
+  merge_group:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  NXF_ANSI_LOG: false
+  NFT_VER: "0.9.2"
+
+jobs:
+  nf-test:
+    name: "nf-test | NXF ${{ matrix.NXF_VER }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: nf-test test --profile test,docker

pipelines/nf-atacseq/README.md

@@ -1,6 +1,6 @@
 # nf-atacseq
 
-[![nf-atacseq Tests](https://github.com/your-org/WASP2/actions/workflows/nf-atacseq-tests.yml/badge.svg)](https://github.com/your-org/WASP2/actions/workflows/nf-atacseq-tests.yml)
+[![nf-atacseq CI](https://github.com/mcvickerlab/WASP2/actions/workflows/ci.yml/badge.svg)](https://github.com/mcvickerlab/WASP2/actions/workflows/ci.yml)
 
 ATAC-seq Allelic Imbalance (AI) Pipeline with WASP2 mapping bias correction.
 
@@ -60,6 +60,12 @@ nextflow run pipelines/nf-atacseq -profile test,docker
 nextflow run pipelines/nf-atacseq -profile test,docker -stub-run  # Workflow validation only
 ```
 
+### Local Test (chr21 data)
+
+```bash
+nextflow run pipelines/nf-atacseq -profile test_local,docker
+```
+
 ## Samplesheet Format
 
 ```csv
@@ -112,6 +118,19 @@ results/
 
 See [docs/output.md](docs/output.md) for detailed output descriptions.
 
+## Validation with chr21 1000 Genomes Data
+
+Run a quick validation using chr21 data from the 1000 Genomes Project:
+
+```bash
+# Uses pre-configured chr21 test data (NA12878, HG00096)
+nextflow run pipelines/nf-atacseq -profile test_local,docker
+
+# Expect: ~2-5 min runtime, allele counts at chr21 het SNPs
+```
+
+This profile uses downsampled chr21 FASTQ reads and a chr21-only VCF, providing a fast end-to-end validation without downloading full genomes.
+
 ## Testing
 
 ### Run nf-test Suite
@@ -148,6 +167,7 @@ nextflow run . -profile test -stub-run
 | `singularity` | Run with Singularity containers |
 | `conda` | Run with Conda environments |
 | `test` | Minimal test configuration |
+| `test_local` | Local test with chr21 1000 Genomes data |
 | `test_full` | Full test with real data |
 
 ## Pipeline DAG
@@ -168,7 +188,7 @@ FASTQ → FastQC → Fastp → BWA/Bowtie2 → Samtools → Picard → MACS2 →
 
 If you use nf-atacseq, please cite:
 
-- **WASP2**: [GitHub Repository](https://github.com/your-org/WASP2)
+- **WASP2**: [GitHub Repository](https://github.com/mcvickerlab/WASP2)
 - **Nextflow**: Di Tommaso, P., et al. (2017). Nextflow enables reproducible computational workflows. *Nature Biotechnology*.
 
 ## License
@@ -177,5 +197,5 @@ MIT License - see [LICENSE](../../LICENSE) for details.
 
 ## Support
 
-- [Issues](https://github.com/your-org/WASP2/issues)
+- [Issues](https://github.com/mcvickerlab/WASP2/issues)
 - [Documentation](docs/)

pipelines/nf-atacseq/assets/email_template.html

@@ -0,0 +1,48 @@
+<html>
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>${workflow.manifest.name} Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+
+<img src="cid:nfcorepipelinelogo">
+
+<h1>${workflow.manifest.name} v${workflow.manifest.version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success) { %>
+<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+<h4 style="color: inherit; margin-top: 0;">⚠️ ${workflow.manifest.name} execution completed unsuccessfully!</h4>
+<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+<p>The full error message was:</p>
+<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+</div>
+<% } else { %>
+<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+${workflow.manifest.name} execution completed successfully!
+</div>
+<% } %>
+
+<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+<p>The command used to launch the workflow was as follows:</p>
+<pre style="white-space: pre-wrap; overflow: visible;">$commandLine</pre>
+
+<h3>Pipeline Configuration:</h3>
+<table cellpadding="5" style="width:100%; max-width:600px; border-collapse: collapse;">
+<tr><td>Nextflow Version</td><td>$nextflowVersion</td></tr>
+<tr><td>Run Name</td><td>$runName</td></tr>
+<tr><td>Session ID</td><td>$sessionId</td></tr>
+<% if (summary.size() > 0) { %>
+<% for (e in summary) { %><tr><td>${e.key}</td><td>${e.value}</td></tr>
+<% } %>
+<% } %>
+</table>
+
+<p>--- <em>${workflow.manifest.name}</em></p>
+
+</div>
+</body>
+</html>

pipelines/nf-atacseq/assets/email_template.txt

@@ -0,0 +1,34 @@
+----------------------------------------------------
+                            ${workflow.manifest.name} v${workflow.manifest.version}
+----------------------------------------------------
+Run Name: $runName
+
+<% if (success) {
+    out << "## ${workflow.manifest.name} execution completed successfully! ##"
+} else {
+    out << """####################################################
+## ${workflow.manifest.name} execution completed unsuccessfully! ##
+####################################################
+The exit status of the task that caused the workflow execution to fail was: $exitStatus.
+The full error message was:
+
+${errorReport}
+"""
+} %>
+
+
+The workflow was completed at $dateComplete (duration: $duration)
+
+The command used to launch the workflow was as follows:
+
+  $commandLine
+
+
+
+Pipeline Configuration:
+-----------------------
+<% for (e in summary) { %>  ${e.key.padRight(30)}: ${e.value}
+<% } %>
+
+--
+${workflow.manifest.name}

pipelines/nf-atacseq/assets/multiqc_config.yml

@@ -1,14 +1,17 @@
 # MultiQC configuration for nf-atacseq
 
 report_comment: >
-    This report has been generated by the <a href="https://github.com/your-org/WASP2" target="_blank">nf-atacseq</a>
-    pipeline. It summarizes QC metrics from ATAC-seq allelic imbalance analysis with WASP2.
+    This report has been generated by the <a href="https://github.com/nf-core/nf-atacseq/releases/tag/1.0.0" target="_blank">nf-core/nf-atacseq</a>
+    analysis pipeline. For information about how to interpret these results, please see the
+    <a href="https://nf-co.re/nf-atacseq/1.0.0/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
-    software_versions:
-        order: -1000
     nf-atacseq-methods-description:
+        order: -1000
+    software_versions:
         order: -1001
+    wasp2-nf-atacseq-summary:
+        order: -1002
 
 export_plots: true
 

pipelines/nf-atacseq/conf/modules.config

@@ -45,7 +45,6 @@ process {
     //
     withName: 'BWA_MEM' {
         ext.args = '-M'
-        ext.args2 = '-bhS'
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,
@@ -63,6 +62,10 @@ process {
         ]
     }
 
+    withName: 'SAMTOOLS_SORT' {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+
     withName: 'SAMTOOLS_INDEX' {
         publishDir = [
             path: { "${params.outdir}/alignment" },

pipelines/nf-atacseq/conf/test_local.config

@@ -37,3 +37,12 @@ params {
     wasp_min_count    = 1
     wasp_pseudocount  = 1
 }
+
+// Override base.config resourceLimits so local workstations don't OOM
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: 6.GB,
+        time: 1.h
+    ]
+}

pipelines/nf-atacseq/environment.yml

@@ -0,0 +1,23 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+# Conda environment for nf-atacseq local Python/WASP2 modules
+# (wasp2_make_reads, wasp2_filter_remapped, wasp2_count_variants, wasp2_find_imbalance)
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python>=3.10
+  - numpy>=1.21,<2.0
+  - pandas>=2.0
+  - polars>=0.19
+  - scipy>=1.10
+  - pysam
+  - pybedtools
+  - samtools
+  - bcftools
+  - bedtools
+  - typer
+  - rich
+  - pip
+  - pip:
+    - wasp2==1.2.1