Introduction Usage Parameters Output

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

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

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

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.

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

required
type: string

Path to reference fast file.

type: string

Reference genome name.

required
type: string

List of tools for running the pipeline.

type: string
default: mobster,viber,pyclone-vi,sparsesignatures,sigprofiler

Method used to save pipeline results to output directory.

type: string
default: copy

Flag for filtering QC mutations or not.

type: string

type: string

Path to VEP cache.

type: string

VEP cache version.

type: string

VEP species.

type: string

VEP reference genome name.

type: string

Add an extra custom argument to VEP.

type: string
default: --everything --filter_common --per_gene --total_length --offline --format vcf

Path to driver table.

type: string
default: https://raw.githubusercontent.com/nicola-calonaci/test-datasets/evoverse/data/DRIVER_ANNOTATION/DNDSCV/RefCDS_human_GRCh38_GencodeV18_recommended.rda

Flag for filtering mutations from vcf.

type: string
default: TRUE

type: string
default: c(\'1:0\', \'1:1\', \'2:0\', \'2:1\', \'2:2\')
type: integer
type: integer
default: 100
type: number
default: 0.005
type: string
default: NULL
type: number
default: 0.05
type: number
default: 0.015
type: integer
default: 1
type: string
default: rightmost
type: string
default: TRUE
type: string
default: 1:1
type: string
default: absolute
type: integer
default: 25
type: number
default: 0.1
type: string
default: FALSE
type: string
default: ENTROPY
type: integer
default: 1

type: string
default: FALSE
type: string
default: TRUE

type: string
default: beta-binomial
type: integer
default: 100
type: integer
default: 100
type: integer
default: 20

type: string
default: 1:5
type: string
default: peaks
type: integer
default: 5
type: string
default: c(TRUE,FALSE)
type: number
default: 1e-10
type: integer
default: 250
type: string
default: MM
type: integer
default: 12345
type: string
default: reICL
type: string
default: FALSE
type: string
default: TRUE
type: number
default: 0.02
type: integer
default: 10
type: string
default: FALSE
type: string
default: NULL

type: integer
default: 10
type: integer
default: 10
type: number
default: 0.000001
type: integer
default: 1
type: integer
default: 1
type: integer
default: 5000
type: number
default: 1e-10
type: string
default: prior
type: string
default: FALSE
type: number
default: 0.05
type: number
default: 0.02
type: string
default: FALSE
type: integer
default: 1

type: integer
default: 10000
type: integer
default: 5000
type: integer
default: 100

type: string
default: 2:10
type: string
default: NULL
type: string
default: NULL
type: string
default: TRUE
type: integer
default: 30
type: integer
default: 10
type: integer
default: 10000
type: string
default: all
type: number
default: 0.01
type: integer
default: 50
type: integer
default: 5
type: string
default: c(0.01, 0.05, 0.1, 0.2)
type: integer
type: string
default: TRUE
type: integer
default: 12345
type: string
default: c(0.00, 0.01, 0.05, 0.10)

Mode of publishing the SigProfiler genome.

type: string
default: move
type: boolean
default: true
type: string
type: boolean
type: string
default: matrix
type: integer
default: 1
type: integer
default: 25
type: string
default: 96,DINUC,ID
type: integer
default: 100
type: boolean
default: true
type: string
default: gmm
type: string
default: random
type: integer
default: 10000
type: integer
default: 1000000
type: integer
default: 10000
type: string
default: random
type: number
default: 0.8
type: integer
default: -1
type: number
default: 0.2
type: integer
default: 1
type: boolean
default: true
type: boolean
default: true
type: number
default: 3.4
type: boolean
default: true
type: boolean
default: true
type: boolean
type: string
default: None
type: boolean
type: boolean
type: string
default: single
type: integer
default: 100
type: boolean
type: boolean
type: integer
default: 1
type: boolean
type: number
default: 1e-15
type: string
default: s3://ngi-igenomes/igenomes/

type: integer
default: 3
type: number
default: 0.75
type: string
default: c(0, 0.7)
type: number
default: 0.6
type: integer
default: 20000
type: string
default: TRUE

Email address for completion summary.

type: boolean

Email address for completion summary, only when pipeline fails.

type: boolean
type: boolean

Do not use coloured log outputs.

type: boolean

Send plain-text email instead of HTML.

type: boolean

Git commit id for Institutional configs.

type: string
default: master

Base directory for Institutional configs.

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

Institutional config description.

type: boolean

Institutional config contact information.

type: boolean

Institutional config URL link.

type: boolean

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

type: string
default: 128 GB

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

type: integer
default: 16

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

type: string
default: 10d
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