Define where the pipeline should find input data and save output data.

Starting step

required
type: string

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

type: string
pattern: ^\S+\.csv$

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

required
type: string

Most common options used for the pipeline

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

type: integer
default: 50000000

Enable when exome or panel data is provided.

type: boolean

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

type: string

Estimate interval size.

type: number
default: 200000

Disable usage of intervals.

type: boolean

Tools to use for variant calling and/or for annotation.

type: string

Disable specified tools.

type: string

Trim fastq file or handle UMIs

Run FastP for read trimming

hidden
type: boolean

Remove bp from the 5’ end of read 1

hidden
type: integer

Remove bp from the 5’ end of read 2

hidden
type: integer

Remove bp from the 3’ end of read 1

hidden
type: integer

Remove bp from the 3’ end of read 2

hidden
type: integer

Removing poly-G tails.

hidden
type: integer

Save trimmed FastQ file intermediates.

hidden
type: boolean

Specify UMI read structure

hidden
type: string

Default strategy with UMI

hidden
type: string
default: Adjacency

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

hidden
type: boolean

Configure preprocessing tools

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

hidden
type: string

Save mapped files.

type: boolean

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

type: boolean

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

type: string

Configure variant calling tools

Option for concatenating germline vcf-files.

type: boolean

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.

type: boolean

Turn on the joint germline variant calling for GATK haplotypecaller

type: boolean

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

hidden
type: number
default: 20

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

hidden
type: number
default: 10

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

hidden
type: number
default: 35

Overwrite ASCAT ploidy.

hidden
type: number

Overwrite ASCAT purity.

hidden
type: number

Specify a custom chromosome length file.

hidden
type: string

Overwrite Control-FREEC coefficientOfVariation

hidden
type: number
default: 0.05

Overwrite Control-FREEC contaminationAdjustement

hidden
type: boolean

Design known contamination value for Control-FREEC

hidden
type: number

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

hidden
type: number

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

hidden
type: number

Genome ploidy used by ControlFREEC

hidden
type: string
default: 2

Overwrite Control-FREEC window size.

hidden
type: number

Copy-number reference for CNVkit

hidden
type: string

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

hidden
type: string

Index of PON panel-of-normals VCF.

hidden
type: string

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

hidden
type: boolean

Allow usage of fasta file for annotation with VEP

hidden
type: boolean

Enable the use of the VEP dbNSFP plugin.

hidden
type: boolean

Path to dbNSFP processed file.

hidden
type: string

Path to dbNSFP tabix indexed file.

hidden
type: string

Consequence to annotate with

hidden
type: string

Fields to annotate with

hidden
type: string
default: rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF

Enable the use of the VEP LOFTEE plugin.

hidden
type: boolean

Enable the use of the VEP SpliceAI plugin.

hidden
type: boolean

Path to spliceai raw scores snv file.

hidden
type: string

Path to spliceai raw scores snv tabix indexed file.

hidden
type: string

Path to spliceai raw scores indel file.

hidden
type: string

Path to spliceai raw scores indel tabix indexed file.

hidden
type: string

Enable the use of the VEP SpliceRegion plugin.

hidden
type: boolean

Add an extra custom argument to VEP.

hidden
type: string

Path to snpEff cache.

hidden
type: string

Path to VEP cache.

hidden
type: string

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

hidden
type: string

VEP output-file format.

hidden
type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string
default: GATK.GRCh38

ASCAT genome.

hidden
type: string

Path to ASCAT allele zip file.

hidden
type: string

Path to ASCAT loci zip file.

hidden
type: string

Path to ASCAT GC content correction file.

hidden
type: string

Path to ASCAT RT (replictiming) correction file.

hidden
type: string

Path to BWA mem indices.

hidden
type: string

Path to bwa-mem2 mem indices.

hidden
type: string

Path to chromosomes folder used with ControLFREEC.

hidden
type: string

Path to dbsnp file.

hidden
type: string

Path to dbsnp index.

hidden
type: string

label string for VariantRecalibration (haplotypecaller joint variant calling)

type: string

Path to FASTA dictionary file.

hidden
type: string

Path to dragmap indices.

hidden
type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Path to FASTA reference index.

type: string

Path to GATK Mutect2 Germline Resource File.

hidden
type: string

Path to GATK Mutect2 Germline Resource Index.

hidden
type: string

Path to known indels file.

hidden
type: string

Path to known indels file index.

hidden
type: string

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

1st label string for VariantRecalibration (haplotypecaller joint variant calling)

type: string

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

Path to known snps file.

type: string

Path to known snps file snps.

type: string

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

label string for VariantRecalibration (haplotypecaller joint variant calling)

type: string

Path to Control-FREEC mappability file.

hidden
type: string

snpEff DB version.

hidden
type: number

snpEff genome.

hidden
type: string

snpEff version.

hidden
type: string

VEP genome.

hidden
type: string

VEP species.

hidden
type: string

VEP cache version.

hidden
type: number

VEP version.

hidden
type: string

Save built references.

type: boolean

Only built references.

type: boolean

Download annotation cache.

type: boolean

Directory / URL base for iGenomes references.

type: string
default: s3://ngi-igenomes/igenomes/

Do not load the iGenomes reference config.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Base path / URL for data used in the test profiles

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/sarek3

Sequencing center information to be added to read group (CN field).

hidden
type: string

Sequencing platform information to be added to read group (PL field).

hidden
type: string
default: ILLUMINA

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

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

type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string