A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation, specifically designed for BigBio workflows.
Note: This repository complements nf-core/modules and does not replace it. BigBio workflows follow a module resolution strategy:
- First priority: Use nf-core modules if available
- Second priority: Use BigBio shared modules (this repository) if available
- Third priority: Use local modules in the workflow repository
The module files hosted in this repository define a set of processes for software tools used in BigBio workflows. These modules follow nf-core module standards and can be shared across multiple BigBio pipelines in a modular fashion.
- Install the latest version of
nf-core/tools(>=2.0) - List the available modules from this repository:
$ nf-core modules list remote --github-repo bigbio/nf-modules
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nf-core/tools version 2.0
INFO Modules available from bigbio/nf-modules (main): pipeline_modules.py:164
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ thermorawfileparser │
│ ... │- Install the module in your pipeline directory:
$ nf-core modules install thermorawfileparser --github-repo bigbio/nf-modules
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nf-core/tools version 2.0
INFO Installing thermorawfileparser pipeline_modules.py:213
INFO Downloaded 3 files to ./modules/bigbio/thermorawfileparser pipeline_modules.py:236- Import the module in your Nextflow script:
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { THERMORAWFILEPARSER } from './modules/bigbio/thermorawfileparser/main'- Remove the module from the pipeline repository if required:
$ nf-core modules remove thermorawfileparser --github-repo bigbio/nf-modules
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nf-core/tools version 2.0
INFO Removing thermorawfileparser pipeline_modules.py:271
INFO Successfully removed thermorawfileparser pipeline_modules.py:285- Check that a locally installed BigBio module is up-to-date compared to the one hosted in this repo:
$ nf-core modules lint thermorawfileparser --github-repo bigbio/nf-modules
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nf-core/tools version 2.0
INFO Linting pipeline: . lint.py:104
INFO Linting module: thermorawfileparser lint.py:106
╭─────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Warning │
╰─────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
│ Module name │ Test message │ File path │
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
│ thermorawfileparser │ Local copy of module outdated │ modules/bigbio/thermorawfileparser/ │
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
╭──────────────────────╮
│ LINT RESULTS SUMMARY │
├──────────────────────┤
│ [✔] 15 Tests Passed │
│ [!] 1 Test Warning │
│ [✗] 0 Test Failed │
╰──────────────────────╯If you wish to contribute a new module, please see the documentation on the nf-core website for module development guidelines.
Please be kind to our code reviewers and submit one pull request per module :)
All modules must:
- Follow nf-core module standards and structure
- Include comprehensive documentation in
meta.yml - Include test files in the
tests/directory - Pass all CI/CD checks before merging
- Be formatted according to
.editorconfigand.prettierrc.yml
BigBio workflows follow a hierarchical module resolution strategy to maximize code reuse and maintainability:
-
nf-core modules (
modules/nf-core/): Use modules from the official nf-core/modules repository when available. These are community-maintained, well-tested modules. -
BigBio shared modules (
modules/bigbio/): Use modules from this repository for BigBio-specific tools or workflows that aren't available in nf-core. These modules follow nf-core standards and are shared across BigBio workflows. -
Local modules (
modules/local/): Use workflow-specific modules only when neither nf-core nor BigBio modules are available. These should be considered for promotion to BigBio modules if they become useful for multiple workflows.
This strategy ensures:
- Maximum code reuse across workflows
- Consistent module quality and standards
- Easy maintenance and updates
- Clear separation between community and BigBio-specific modules
This repository follows the nf-core modules repository structure:
nf-modules/
├── modules/
│ └── bigbio/ # BigBio-specific modules
├── tests/ # Module tests
│ ├── config/ # Test configurations
│ └── modules/ # Module-specific tests
├── .github/
│ └── workflows/ # CI/CD workflows
└── docs/ # Documentation
For further information or help, please:
- Open an issue on GitHub
- Check the nf-core documentation for module development guidelines
- Join the BigBio community discussions
If you use the module files in this repository for your analysis, please cite:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Additionally, if you use BigBio-specific modules, please cite this repository:
BigBio nf-modules: Shared Nextflow modules for BigBio workflows.
BigBio Community.
GitHub: bigbio/nf-modules
This project is licensed under the MIT License - see the LICENSE file for details.