Add MultiQC plugin for DCQC validation results

conf/modules.config

@@ -47,4 +47,12 @@ process {
         ]
     }
 
+    withName: MULTIQC {
+        ext.args = "--export"
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode
+        ]
+    }
+
 }

modules/local/multiqc.nf

@@ -0,0 +1,69 @@
+process MULTIQC {
+    label 'process_single'
+
+    conda "bioconda::multiqc=1.15"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.15--pyhdfd78af_0' }"
+
+    input:
+    path suites_json
+    path multiqc_config
+    path plugin_dir
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    # Set up local Python environment
+    export PYTHONUSERBASE=\${PWD}/.local
+    export PATH=\${PYTHONUSERBASE}/bin:\${PATH}
+
+    # Install the custom MultiQC plugin first
+    cd ${plugin_dir}
+    pip install --user --no-deps .
+    cd -
+
+    # Find the actual site-packages directory and set PYTHONPATH
+    SITE_PACKAGES=\$(find \${PYTHONUSERBASE}/lib -name site-packages -type d | head -n 1)
+    if [ -z "\${PYTHONPATH:-}" ]; then
+        export PYTHONPATH=\${SITE_PACKAGES}
+    else
+        export PYTHONPATH=\${SITE_PACKAGES}:\${PYTHONPATH}
+    fi
+
+    # suites.json is already staged by Nextflow, no need to copy
+
+    # Run MultiQC with the custom config
+    multiqc \\
+        --force \\
+        --config ${multiqc_config} \\
+        $args \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}

multiqc/.gitignore

@@ -0,0 +1,10 @@
+# Python build artifacts
+build/
+dist/
+*.egg-info/
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Setuptools
+.eggs/

multiqc/multiqc_config.yaml

@@ -0,0 +1,10 @@
+# MultiQC Configuration for DCQC Validation Plugin
+
+# Force run the dcqc_validation module
+run_modules:
+  - dcqc_validation
+
+# Search pattern for dcqc_validation (plugin for DCQC validation)
+sp:
+  dcqc_validation:
+    fn: "suites.json"

multiqc/multiqc_dcqc/README.md

@@ -0,0 +1,100 @@
+# MultiQC DCQC Validation Plugin
+
+A MultiQC plugin for displaying validation results from DCQC suite testing.
+
+## Features
+
+- **Validation Summary**: Overview table showing overall status for each validated file
+- **Test Details**: Detailed breakdown of individual test results by suite type
+- **Failed Tests**: Comprehensive error messages and validation failures
+- **General Stats**: Key metrics added to MultiQC general statistics table
+- **Multi-Suite Support**: Handles all DCQC suite types (H5AD, and more)
+
+## Installation
+
+Install the plugin using pip from the project directory:
+
+```bash
+pip install .
+```
+
+Or install in development mode:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+Run MultiQC in a directory containing `suites.json` file(s):
+
+```bash
+multiqc .
+```
+
+Or specify the results directory:
+
+```bash
+multiqc results/
+```
+
+## Data Format
+
+The plugin expects a `suites.json` file with the following structure:
+
+```json
+[
+  {
+    "type": "H5ADSuite",  // or other suite types
+    "target": {
+      "id": "sample_001",
+      "files": [
+        {
+          "name": "sample.h5ad",  // or other file types
+          "url": "...",
+          "local_path": "..."
+        }
+      ]
+    },
+    "suite_status": {
+      "status": "GREEN",
+      "required_tests": [...]
+    },
+    "tests": [
+      {
+        "type": "TestName",
+        "tier": 1,
+        "status": "passed",
+        "status_reason": "",
+        "is_external_test": false
+      }
+    ]
+  }
+]
+```
+
+The plugin supports all DCQC suite types and will display the suite type in the reports.
+
+## Configuration
+
+The plugin automatically searches for `suites.json` files. You can customize the search pattern in your MultiQC configuration file:
+
+```yaml
+sp:
+  dcqc_validation:
+    fn: 'suites.json'
+```
+
+## Output
+
+The plugin generates three main sections in the MultiQC report:
+
+1. **Validation Summary**: High-level overview with pass/fail status for each file and suite type
+2. **Test Details**: Individual test results for each file, organized by suite type
+3. **Failed Tests**: Detailed error messages for any failed validation tests
+
+All sections display the suite type to help distinguish between different validation workflows (e.g., H5ADSuite, etc.).
+
+## License
+
+MIT

multiqc/multiqc_dcqc/__init__.py

@@ -0,0 +1,26 @@
+"""
+MultiQC plugin for DCQC validation results.
+"""
+
+from multiqc.utils import config
+
+# Make sure this plugin runs after any standard MultiQC modules
+config.module_order.append(
+    {
+        "dcqc_validation": {
+            "module_tag": ["QC", "Validation"],
+            "name": "DCQC Validation",
+            "anchor": "dcqc-validation",
+            "target": "DCQC Validation",
+            "info": "displays validation results from DCQC suite testing",
+        }
+    }
+)
+
+# Configure search patterns for finding suites.json files
+config.sp["dcqc_validation"] = {
+    "fn": "suites.json",
+}
+
+# Import the module
+from multiqc_dcqc import dcqc_validation