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Nextflow Examples

Common usage patterns for the gbcms Nextflow pipeline.

DNA Mode (Default)

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

RNA Mode

Basic RNA-seq

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

RNA with Editing Database

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.maf \
    --fasta reference.fa \
    --mode rna \
    --format maf \
    --rna_editing_db /path/to/TABLE1_hg38_v3.txt \
    --enforce_strandedness \
    -profile docker

MAF Output

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

Strict Filtering

Enable additional read filters beyond the defaults (duplicates, secondary, supplementary, and QC-failed are already on by default):

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

UMI-Aware Counting

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    --umi_tag XM \
    -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