Nextflow Vdsl3 Platform

Next-gen platform for generating NextFlow VDSL3 modules.

auto

Type: NextflowAuto

Automated processing flags which can be toggled on or off:

Flag Description Default
simplifyInput If true, an input tuple only containing only a single File (e.g. ["foo", file("in.h5ad")]) is automatically transformed to a map (i.e. ["foo", [ input: file("in.h5ad") ] ]). true
simplifyOutput If true, an output tuple containing a map with a File (e.g. ["foo", [ output: file("out.h5ad") ] ]) is automatically transformed to a map (i.e. ["foo", file("out.h5ad")]). true
transcript If true, the module’s transcripts from work/ are automatically published to params.transcriptDir. If not defined, params.publishDir + "/_transcripts" will be used. Will throw an error if neither are defined. false
publish If true, the module’s outputs are automatically published to params.publishDir. Will throw an error if params.publishDir is not defined. false

Example:

auto:
    publish: true

container

Type: String

Specifies the Docker platform id to be used to run Nextflow.

debug

Type: Boolean

Whether or not to print debug messages.

directives

Type: NextflowDirectives

Directives are optional settings that affect the execution of the process. These mostly match up with the Nextflow counterparts that are linked below:

Example:

directives:
    container: rocker/r-ver:4.1
    label: highcpu
    cpus: 4
    memory: 16 GB

id

Type: String

Every platform can be given a specific id that can later be referred to explicitly when running or building the Viash component.

Example:

id: foo

type

Type: String

Specifies the type of the platform.