Nextflow Examples

Common workflows for batch processing with Krewlyzer.

Basic Run

nextflow run msk-access/krewlyzer \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --outdir results/

MSK-ACCESS Panel

nextflow run msk-access/krewlyzer \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --asset_dir /path/to/krewlyzer/data/ \
    --outdir results/

With samplesheet:

sample,bam,meth_bam,vcf,bed,maf,single_sample_maf,assay,pon,targets
ACCESS_001,/data/sample1.bam,,,,,false,XS2,,
ACCESS_002,/data/sample2.bam,,,,,false,XS2,,

With Variant Analysis

nextflow run msk-access/krewlyzer \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --outdir results/

With samplesheet:

sample,bam,meth_bam,vcf,bed,maf,single_sample_maf,assay,pon,targets
SAMPLE_001,/data/sample1.bam,,,/data/variants.vcf,,,XS2,,
SAMPLE_002,/data/sample2.bam,,,,/data/cohort.maf,false,XS2,,

Using Docker

nextflow run msk-access/krewlyzer \
    -profile docker \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --outdir results/

SLURM Cluster

nextflow run msk-access/krewlyzer \
    -profile slurm \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --outdir results/

IRIS HPC (MSK)

For running on MSKCC's IRIS cluster, use the nf-core/configs institutional profile:

nextflow run msk-access/krewlyzer \
    -profile iris \
    --samplesheet samples.csv \
    --ref /data1/ref/hg19/hg19.fa \
    --outdir /scratch/$GROUP/results/

Tip

The iris profile automatically configures: - SLURM executor with proper queue settings - Singularity with pre-cached images at /data1/core006/resources/singularity_image_library - Scratch paths and work directories

For preemptable (faster) queue:

nextflow run msk-access/krewlyzer \
    -profile iris \
    --preemptable true \
    --samplesheet samples.csv \
    --ref /data1/ref/hg19/hg19.fa \
    --outdir /scratch/$GROUP/results/

Resume Failed Run

nextflow run msk-access/krewlyzer \
    -resume \
    --samplesheet samples.csv \
    --ref /path/to/hg19.fa \
    --outdir results/