Modules

Repository Structure

.
├── README.md
├── main.nf
└── modules
    └── UMCUGenetics
└── subworkflows
    └── UMCUGenetics

Modules are placed under the ./modules/UMCUGenetics/ folder in the format tool/subtool. For example ./modules/UMCUGenetics/samtools/view/ Similarly, subworkflows are placed under the subworkflows/UMCUGenetics/ folder. Preferably a subworkflow is named INPUT_DESCRIPTION For example ./subworkflows/UMCUGenetics/bam_prs/ or ./subworkflows/UMCUGenetics/vcf_ancestry/

Linting

To lint the modules and subworkflows nf-core/tools is used. We use the default linting configuration, except for the meta.yml requirements. The github action for linting (triggered upon creating a PR to main) is already configured to ignore meta.yml checks. To run linting locally with the same settings:

pip install nf-core==4.1.0
nf-core modules lint --key module_tests --key environment_yml --key main_nf --key module_deprecations --key module_tests <tool/name>
nf-core subworkflows lint --key subworkflow_tests --key subworkflow_if_empty_null --key subworkflow_todos --key main_nf <name>

Testing

Module and subworkflow tests are evaluated using nf-test. A github action is configured to automatically run tests upon module/subworkflow change.

Test data

Test data can be hosted on the companion repository https://github.com/UMCUGenetics/DxNextflowTestData. Be aware that this repository is public and should not contain any private data.

Using a module or subworkflow in a nextflow pipeline

Components from this repository can be added to a pipeline similarly to how nf-core components are installed.

nf-core modules --git-remote https://github.com/UMCUGenetics/NF-Modules install pgscatalog/combine
nf-core subworkflows --git-remote https://github.com/UMCUGenetics/NF-Modules install bam_prs

To view all available components:

nf-core modules --git-remote https://github.com/UMCUGenetics/NF-Modules list remote
nf-core subworkflows --git-remote https://github.com/UMCUGenetics/NF-Modules list remote