Nextflow Vdsl3 Platform

Next-gen platform for generating NextFlow VDSL3 modules.

auto

Type: NextflowAuto

Automated processing flags which can be toggled on or off:

  • 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") ] ]). Default is 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")]). Default is 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. Default is false.
  • publish: If true, the module’s outputs are automatically published to params.publishDir. Will throw an error if params.publishDir is not defined. Default is false.

Example

auto:
    publish: true

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