Cross-organisational components

You can specify individual remotes for each module within a subworkflow’s meta.yml file. This allows you to combine components from your own organisation with modules from other sources like nf-core.

This guide explains how to use modules from different organisations within a single subworkflow using nf-core/tools.

Implementation

To mix modules from different sources, configure the meta.yml file with specific remotes for each component.

For example, the fastq_trim_fastp_fastqc subworkflow from nf-core-test organization combines:

• FastQC from the local organisation
• fastp from the nf-core repository

The meta.yml configuration uses this structure:

name: "fastq_trim_fastp_fastqc"
description: Read QC, fastp trimming and read qc
keywords:
  - qc
  - quality_control
  - adapters
  - trimming
  - fastq
components:
  - fastqc
  - fastp:
      git_remote: https://github.com/nf-core/modules.git

This tells nf-core/tools to install FastQC from the same repository as the subworkflow, while fastp comes from the nf-core/modules remote.

Installation

When you install subworkflows from non-nf-core organisations, include the --git-remote parameter in your command.

Schema configuration

For cross-organisational subworkflows, update your JSON schema to allow both object and string types in the components section. This enables the flexible syntax shown above.

"components": {
  "type": "array",
  "description": "Modules and subworkflows used in the subworkflow",
  "items": {
    "type": ["object", "string"]
  },
  "minItems": 0
},