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Process Guide

Parameters

The Parameters section is where you define the parameters that your process will use when specifying its inputs and outputs. You can create new parameters using the Add Parameter button.

Add parameter

Identifier

  • The Identifier is the name of the parameter.
  • Once created, the same parameter can be referenced and reused in other processes.

Qualifier

Via Foundry supports five main qualifier types:

  • file / path
  • set / tuple
  • val
  • each
  • env

These qualifiers correspond directly to Nextflow input semantics.

file / path

Use file when the parameter represents a file input.

Example usage in a Nextflow process:

file genome

set / tuple

Use set / tuple to handle a group of input values together, often combining different qualifiers.

Example:

tuple val(name), file(genome)
tuple val(name), file(bam), file(bam_index)

val

Use val for simple values (such as strings, numbers, flags) that you want to access by name in the process script.

Example:

val script_path

each

Use each to run the process once for each entry in an input collection.

Example:

each bed_list

env

Use env to inject a value into the environment of the process (for example, environment variables). (Behavior follows standard Nextflow env semantics.)

File Type

If the qualifier is set to file or set / tuple, a File type field becomes available.

  • File type is used to filter compatible nodes when building pipelines.
  • This helps ensure that only parameters with matching file types can be connected.

Tips and Notes

Tip

For example:

  • To create a genome parameter:

    • Identifier: genome
    • Qualifier: file
    • File type: fasta

  • To create a script_path parameter:

    • Identifier: script_path
    • Qualifier: val

Note

  • When the qualifier is val, the identifier is used to filter available nodes when connecting parameters.
  • When the qualifier is file or set / tuple, the file type is used to filter available nodes.

  • When the qualifier is each, you may:

    • Use file type if it connects to file-based nodes.
    • Use identifier if it connects to val-type nodes.