nf-core/sarek

Path to comma-separated file containing information about the samples in the experiment.

Starting step

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.

Estimate interval size.

Path to target bed file in case of whole exome or targeted sequencing or intervals file.

Disable usage of intervals.

Enable when exome or panel data is provided.

Tools to use for duplicate marking, variant calling and/or for annotation.

Disable specified tools.

Run FastP for read trimming

Remove bp from the 5’ end of read 1

Remove bp from the 5’ end of read 2

Remove bp from the 3’ end of read 1

Remove bp from the 3’ end of read 2

Removing poly-G tails.

Minimum length of reads to keep

Save trimmed FastQ file intermediates.

Specify UMI read structure

Default strategy with UMI

If set, publishes split FASTQ files. Intended for testing purposes.

Specify aligner to be used to map reads to reference genome.

Save mapped files.

Saves output from mapping (if --save_mapped), Markduplicates & Baserecalibration as BAM file instead of CRAM

Enable usage of GATK Spark implementation for duplicate marking and/or base quality score recalibration

If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools.

Overwrite Ascat min base quality required for a read to be counted.

Overwrite Ascat minimum depth required in the normal for a SNP to be considered.

Overwrite Ascat min mapping quality required for a read to be counted.

Overwrite ASCAT ploidy.

Overwrite ASCAT purity.

Specify a custom chromosome length file.

Overwrite Control-FREEC coefficientOfVariation

Overwrite Control-FREEC contaminationAdjustement

Design known contamination value for Control-FREEC

Minimal sequencing quality for a position to be considered in BAF analysis.

Minimal read coverage for a position to be considered in BAF analysis.

Genome ploidy used by ControlFREEC

Overwrite Control-FREEC window size.

Copy-number reference for CNVkit

Turn on the joint germline variant calling for GATK haplotypecaller

Runs Mutect2 in joint (multi-sample) mode for better concordance among variant calls of tumor samples from the same patient. Mutect2 outputs will be stored in a subfolder named with patient ID under variant_calling/mutect2/ folder. Only a single normal sample per patient is allowed. Tumor-only mode is also supported.

Do not analyze soft clipped bases in the reads for GATK Mutect2.

Panel-of-normals VCF (bgzipped) for GATK Mutect2

Index of PON panel-of-normals VCF.

Option for selecting output and emit-mode of Sentieon’s Haplotyper.

Option for selecting output and emit-mode of Sentieon’s Dnascope.

Option for selecting the PCR indel model used by Sentieon Dnascope.

Option for concatenating germline vcf-files.

Allow usage of fasta file for annotation with VEP

Enable the use of the VEP dbNSFP plugin.

Path to dbNSFP processed file.

Path to dbNSFP tabix indexed file.

Consequence to annotate with

Fields to annotate with

Enable the use of the VEP LOFTEE plugin.

Enable the use of the VEP SpliceAI plugin.

Path to spliceai raw scores snv file.

Path to spliceai raw scores snv tabix indexed file.

Path to spliceai raw scores indel file.

Path to spliceai raw scores indel tabix indexed file.

Enable the use of the VEP SpliceRegion plugin.

Add an extra custom argument to VEP.

Should reflect the VEP version used in the container.

The output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.

VEP output-file format.

A vcf file containing custom annotations to be used with bcftools annotate. Needs to be bgzipped.

Index file for bcftools_annotations

Text file with the header lines of bcftools_annotations

The base path to the igenomes reference files

Do not load the iGenomes reference config.

Save built references.

Only built references.

Download annotation cache.

Name of iGenomes reference.

ASCAT genome.

Path to ASCAT allele zip file.

Path to ASCAT loci zip file.

Path to ASCAT GC content correction file.

Path to ASCAT RT (replictiming) correction file.

Path to BWA mem indices.

Path to bwa-mem2 mem indices.

Path to chromosomes folder used with ControLFREEC.

Path to dbsnp file.

Path to dbsnp index.

Label string for VariantRecalibration (haplotypecaller joint variant calling).

If you use AWS iGenomes, this has already been set for you appropriately.

Path to FASTA dictionary file.

Path to dragmap indices.

Path to FASTA genome file.

Path to FASTA reference index.

Path to GATK Mutect2 Germline Resource File.

Path to GATK Mutect2 Germline Resource Index.

Path to known indels file.

Path to known indels file index.

Label string for VariantRecalibration (haplotypecaller joint variant calling). If you use AWS iGenomes, this has already been set for you appropriately.

Path to known snps file.

Path to known snps file snps.

Label string for VariantRecalibration (haplotypecaller joint variant calling).If you use AWS iGenomes, this has already been set for you appropriately.

Path to Control-FREEC mappability file.

Path to SNP bed file for sample checking with NGSCheckMate

Machine learning model for Sentieon Dnascope.

Path to snpEff cache.

snpEff DB version.

Path to VEP cache.

VEP cache version.

VEP genome.

VEP species.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Custom MultiQC yaml file containing HTML including a methods description.