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Nextflow Examples

Common usage patterns for the gbcms Nextflow pipeline.

Basic Usage

Local with Docker

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    --outdir results \
    -profile docker

SLURM Cluster

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    --outdir results \
    -profile slurm

MAF Output

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants input.maf \
    --fasta reference.fa \
    --format maf \
    -profile docker

Strict Filtering

Enable all quality filters:

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    --filter_duplicates true \
    --filter_secondary true \
    --filter_supplementary true \
    --filter_qc_failed true \
    -profile docker

Multi-Sample MAF Filtering

Filter a multi-sample MAF so each BAM only processes its own variants:

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants multi_sample.maf \
    --fasta reference.fa \
    --format maf \
    --filter_by_sample \
    -profile docker

With patient-level filtering via tsb column in samplesheet:

sample,bam,tsb
patient_A,/path/to/A.bam,P-0012345
patient_B,/path/to/B.bam,"P-0067890-T01,P-0067890-T02"

See Samplesheet — Multi-Sample MAF Filtering for details.

Resume Failed Run

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    -profile docker \
    -resume

Custom Resource Limits

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    --max_cpus 8 \
    --max_memory 32.GB \
    -profile docker