Nextflow Examples

Common usage patterns for the py-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

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

Related

• Samplesheet — Input format

• Parameters — All options

• CLI Quick Start — For few samples