Introduction Usage Parameters Output

Parameters to modify MEA behavior

Column name for gene ID/names

type: string
default: markname

Column name for p-values

type: string
default: meta_p

Number of tests for multiple testing

type: integer
default: 17551

P-value threshold alpha value

type: number
default: 0.05

Parameters to modify MMAP behavior

Whether MMAP output has a header or not

type: integer
default: 1

Column name or number for p-values

type: string
default: p_vals

Column name or number for Beta values

type: string
default: betas_genes

Column name or number for SE values

type: string
default: se_genes

Parameters to modify PASCAL behavior

Whether PASCAL output has a header or not

type: integer

Column name or number for p-values

type: integer
default: 1

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

path to samplesheet

required
type: string

output directory

type: string
default: results

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

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|d|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, 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

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean
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