Singularity Support for noveltree

This pipeline now supports Singularity/Apptainer for HPC environments!

What was configured

Singularity profile in nextflow.config with:
- Auto-conversion from Docker images (singularity.pullDockerContainer = true)
- Automatic cache directory for Singularity images
- Auto-mounting of filesystems
Lima VM setup for local testing (since Singularity doesn't run on macOS natively)
- VM: apptainer-x86 with Apptainer 1.4.4
- Nextflow 25.10.2 installed
- Java 21 runtime

Run the test script:

./test_singularity.sh

This will run the pipeline's test suite with Singularity in the Lima VM.

On your HPC system, simply use the singularity profile:

nextflow run Arcadia-Science/noveltree \
    -profile singularity \
    --input samplesheet.csv \
    --outdir results

You may want to customize the Singularity cache location for your HPC:

nextflow run Arcadia-Science/noveltree \
    -profile singularity \
    --input samplesheet.csv \
    --outdir results \
    -c custom.config

Where custom.config contains:

singularity {
    cacheDir = '/path/to/shared/singularity/cache'
}

Docker → Singularity Auto-conversion: When you use -profile singularity, Nextflow automatically:
1. Pulls Docker images from the specified registries
2. Converts them to Singularity .sif format
3. Caches them for reuse (in singularity_cache/ by default)