VCF Expression Annotator

Nextflow pipeline that annotates VCF variants with RNA-seq transcript expression data using vcf-expression-annotator. Integrates output from nf-core/rnaseq and nf-core/sarek.

Quick Start

nextflow run main.nf -profile test,docker  # Test run

nextflow run main.nf -profile docker \
    --patient_id 'PID_262622_' \
    --samplesheet samplesheet.csv \
    --transcript_counts salmon.merged.transcript_counts.tsv \
    --outdir results

Requirements: Nextflow ≥23.04.0, Docker/Singularity

Input

Samplesheet CSV (--samplesheet):

sample_id,vcf_path,vcf_tumor_sample
SAMPLE_A,/data/vcfs/sample_A.vcf.gz,PATIENT001_tumor_SAMPLE_A

Transcript counts TSV (--transcript_counts): Output from nf-core/rnaseq at results/star_salmon/salmon.merged.transcript_counts.tsv

Required parameters:

• --patient_id: Patient prefix (must end with _)
• --samplesheet: CSV with sample metadata
• --transcript_counts: Merged transcript counts TSV
• --outdir: Output directory

Output

Annotated VCFs with TX field containing transcript expression:

results/clean_vcf/
├── {sample_id}.clean.vcf    # TX field: ENST00000456328:150.5|ENST00000450305:45.2
└── {sample_id}.clean.csv    # CSV export

Testing

This pipeline uses nf-test for automated testing with the nft-vcf and nft-csv plugins.

Prerequisites

Install nf-test (requires Java 11+):

curl -fsSL https://code.askimed.com/install/nf-test | bash
mv nf-test /usr/local/bin/   # or anywhere on your PATH

Run all tests

nf-test test

This uses the configuration in nf-test.config, which automatically applies the test,docker profile and loads the required plugins.

Run specific tests

# Full pipeline integration test
nf-test test tests/main.nf.test

# Individual module tests
nf-test test tests/modules/split_transcript_counts.nf.test
nf-test test tests/modules/vcf_expression_annotator.nf.test
nf-test test tests/modules/clean_vcf.nf.test
nf-test test tests/modules/vcf_to_csv.nf.test

Test data

Test fixtures live in tests/data/ and the sample sheet used for testing is at tests/samplesheet.csv. The test profile (-profile test) configures paths to these fixtures automatically.

Troubleshooting

• Ensure --patient_id ends with _
• sample_id should NOT include patient_id prefix
• Verify VCF sample names: bcftools query -l file.vcf.gz
• Empty TX field? Check transcript IDs match between VCF and counts file

Citation

Gross, T. (2025). VCF Expression Annotator. https://github.com/tylergross97/vcf_expression_annotation

License

MIT License