Configure test_full profile with default iGenomes references

- Add default reference genome paths from AWS iGenomes (s3://ngi-igenomes)
- Set hg38_fasta to GRCh38 NCBI build
- Set nsg_fasta to mm10 UCSC build
- Makes test_full profile fully self-contained and runnable without additional parameters
- Updated README to document the new default configuration
- Users can still override with custom reference paths if needed (e.g., for NSG-adapted genome)

This change makes the test_full profile much more user-friendly and enables
testing in cloud environments (AWS, Seqera Platform) without local reference setup.

Author: Seqera AI

README.md

@@ -152,7 +152,10 @@ This runs with:
 Test with real PDX WES data from the PDM database:
 
 ```bash
-# Run full test - must provide reference genome paths
+# Run full test using default iGenomes references (recommended)
+nextflow run tylergross97/nextflow_xengsort -profile test_full,docker
+
+# Or override with custom reference paths
 nextflow run tylergross97/nextflow_xengsort \
     -profile test_full,docker \
     --hg38_fasta s3://your-bucket/GRCh38.fa \
@@ -162,12 +165,14 @@ nextflow run tylergross97/nextflow_xengsort \
 This runs with:
 - Real-world PDX WES data (2 samples from PDM database)
 - FASTQ data automatically fetched via URLs (no manual download needed)
-- **Reference genomes must be provided** (not bundled due to large file sizes)
+- **Default reference genomes from AWS iGenomes** (s3://ngi-igenomes)
+  - GRCh38 (NCBI build)
+  - mm10 (UCSC build) - note: NSG-specific features may require custom reference
 - Production-level memory requirements (16-32 GB)
 - ~30-60 minute runtime (depending on download speed and data size)
 - Outputs to `results_test_full/` directory
 
-> **Note**: Reference genomes are not included in the test profile due to their large size. You must provide paths to your own GRCh38 (human) and mm10/NSG (mouse) reference genomes via the `--hg38_fasta` and `--nsg_fasta` parameters.
+> **Note**: The `test_full` profile uses reference genomes from the public AWS iGenomes bucket by default. These are automatically accessible in cloud environments (AWS, Seqera Platform). For NSG-specific PDX models, consider using the NSG-adapted reference genome (see Reference Genomes section) by overriding with `--nsg_fasta`.
 
 ## ⚙️ Parameters
 

nextflow.config

@@ -100,17 +100,11 @@ profiles {
             outdir_xengsort = "results_test_full/xengsort"
             outdir_multiqc = "results_test_full/multiqc"
 
-            // Reference genomes - MUST be provided via command line or launch parameters
-            // These are not bundled due to large file sizes
-            // 
-            // Example command:
-            //   nextflow run tylergross97/nextflow_xengsort \
-            //     -profile test_full,docker \
-            //     --hg38_fasta s3://your-bucket/GRCh38.fa \
-            //     --nsg_fasta s3://your-bucket/mm10_nsg.fa
-            //
-            // Leave as null to force users to specify
-            // hg38_fasta and nsg_fasta inherit from main params block (null by default)
+            // Reference genomes from ngi-igenomes (AWS iGenomes)
+            // Using standard paths in s3://ngi-igenomes bucket (eu-west-1 region)
+            // These can be overridden via command line if needed
+            hg38_fasta = "s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            nsg_fasta = "s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
 
             // Process settings for WES data
             fastp_args = "--detect_adapter_for_pe --cut_front --cut_tail --cut_mean_quality 20"