Using subworkflows with modules from multiple organisations

In order to use cross-organisational subworkflows, you can specify individual remotes to be used for each module within the meta.yml file in that subworkflow.

For example, let’s say you have a subworkflow in your own organisation’s modules repository that uses FastQC and fastp. But, instead of using the fastp module from your own organisation, you want to use nf-core’s fastp module. This is the case for the fastq_trim_fastp_fastqc subworkflow in the nf-core-test organization.

In order to have this subworkflow, with a FastQC module from your organisation and fastp from nf-core, you’d define the components section of this subworkflow’s meta.yml file as such:

meta.yml
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

By using the structure above, nf-core/tools knows that it should install FastQC from the same repository that the subworkflow is located in, but fastp should come from the nf-core/modules remote.

Note

Be aware that to install subworkflows from organisations other than nf-core you must specify --git-remote in the nf-core subworkflows command, e.g. nf-core subworkflows install fastq_trim_fastp_fastqc --git-remote $ORG_NAME

If you’re using cross-organisational subworkflows in your repository, be aware that you must also specify a different JSON schema to lint the meta.yml files for your subworkflows. To do this, just change the components section type to allow both objects and strings.

yaml-schema.json
"components": {
  "type": "array",
  "description": "Modules and subworkflows used in the subworkflow",
  "items": {
    "type": ["object", "string"]
  },
  "minItems": 0
},
Tip

To get the full content for the schema, see the corresponding file in the nf-core-test modules repository.