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: \.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: 1000

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 BAMs.

type: boolean

Saves output from 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

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

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: integer
default: 2

Overwrite Control-FREEC window size.

hidden
type: number

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

Path to snpEff cache.

hidden
type: string

Path to VEP cache.

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: \.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: string

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

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

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

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

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

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean