/nextflow-development

nf-core/sarek

Version: 3.7.1

Official Documentation: https://nf-co.re/sarek/3.7.1/ GitHub: https://github.com/nf-core/sarek

Note: When updating to a new version, check the releases page for breaking changes and update the version in commands below.

Contents

• Test command
• Samplesheet format
• Variant calling modes
• Parameters
• Output files

Test command

nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek

Expected: ~20 min, creates aligned BAMs and variant calls.

Samplesheet format

From FASTQ

patient,sample,lane,fastq_1,fastq_2
patient1,tumor,L001,/path/to/tumor_L001_R1.fq.gz,/path/to/tumor_L001_R2.fq.gz
patient1,tumor,L002,/path/to/tumor_L002_R1.fq.gz,/path/to/tumor_L002_R2.fq.gz
patient1,normal,L001,/path/to/normal_R1.fq.gz,/path/to/normal_R2.fq.gz

From BAM/CRAM

patient,sample,bam,bai
patient1,tumor,/path/to/tumor.bam,/path/to/tumor.bam.bai
patient1,normal,/path/to/normal.bam,/path/to/normal.bam.bai

With tumor/normal status

patient,sample,lane,fastq_1,fastq_2,status
patient1,tumor,L001,tumor_R1.fq.gz,tumor_R2.fq.gz,1
patient1,normal,L001,normal_R1.fq.gz,normal_R2.fq.gz,0

status: 0 = normal, 1 = tumor

Variant calling modes

Germline (single sample)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --tools haplotypecaller,snpeff

Somatic (tumor-normal pair)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --tools mutect2,strelka,snpeff

WES (exome)

nextflow run nf-core/sarek -r 3.7.1 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 \
    --wes --intervals /path/to/targets.bed \
    --tools haplotypecaller,snpeff

Joint germline (cohort)

--tools haplotypecaller --joint_germline

Parameters

Available tools

Germline callers:

• haplotypecaller: GATK HaplotypeCaller
• freebayes: FreeBayes
• deepvariant: DeepVariant (GPU optional)
• strelka: Strelka2 germline

Somatic callers:

• mutect2: GATK Mutect2
• strelka: Strelka2 somatic
• manta: Structural variants

CNV callers:

• ascat: Copy number
• controlfreec: CNV detection
• tiddit: SV calling

Annotation:

• snpeff: Functional annotation
• vep: Variant Effect Predictor

Key parameters

Output files

results/
├── preprocessing/
│   └── recalibrated/           # Analysis-ready BAMs
│       └── *.recal.bam
├── variant_calling/
│   ├── haplotypecaller/        # Germline VCFs
│   ├── mutect2/                # Somatic VCFs (filtered)
│   └── strelka/
├── annotation/
│   └── snpeff/                 # Annotated VCFs
└── multiqc/

Troubleshooting

BQSR fails: Check known sites available for genome. Skip with --skip_bqsr for non-standard references.

Mutect2 no variants: Verify tumor/normal pairing in samplesheet (check status column).

Out of memory: --max_memory '128.GB' for WGS.

DeepVariant GPU: Ensure NVIDIA Docker runtime configured.

More Information

• Full parameter list: https://nf-co.re/sarek/3.7.1/parameters/
• Output documentation: https://nf-co.re/sarek/3.7.1/docs/output/
• Usage documentation: https://nf-co.re/sarek/3.7.1/docs/usage/