A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation.
The module files hosted in this repository define a set of processes for software tools such as fastqc, bwa, samtools etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
We have written a helper command in the nf-core/tools package that uses the GitHub API to obtain the relevant information for the module files present in the modules/ directory of this repository. This includes using git commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.
- Install the latest version of
nf-core/tools(>=2.0) - List the available modules:
$ nf-core modules list remote
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nf-core/tools version 2.0
INFO Modules available from nf-core/modules (master): pipeline_modules.py:164
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ bandage/image │
│ bcftools/consensus │
│ bcftools/filter │
│ bcftools/isec │
..truncated..- Install the module in your pipeline directory:
$ nf-core modules install fastqc
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nf-core/tools version 2.0
INFO Installing fastqc pipeline_modules.py:213
INFO Downloaded 3 files to ./modules/nf-core/modules/fastqc pipeline_modules.py:236- Import the module in your Nextflow script:
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTQC } from './modules/nf-core/modules/fastqc/main'- Remove the module from the pipeline repository if required:
$ nf-core modules remove fastqc
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nf-core/tools version 2.0
INFO Removing fastqc pipeline_modules.py:271
INFO Successfully removed fastqc pipeline_modules.py:285- Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
$ nf-core modules lint fastqc
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nf-core/tools version 2.0
INFO Linting pipeline: . lint.py:104
INFO Linting module: fastqc lint.py:106
╭─────────────────────────────────────────────────────────────────────────────────╮
│ [!] 1 Test Warning │
╰─────────────────────────────────────────────────────────────────────────────────╯
╭──────────────┬───────────────────────────────┬──────────────────────────────────╮
│ Module name │ Test message │ File path │
├──────────────┼───────────────────────────────┼──────────────────────────────────┤
│ fastqc │ Local copy of module outdated │ modules/nf-core/modules/fastqc/ │
╰──────────────┴────────────────────────────── ┴──────────────────────────────────╯
╭──────────────────────╮
│ 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.
Please be kind to our code reviewers and submit one pull request per module :)
For further information or help, don't hesitate to get in touch on Slack #modules channel (you can join with this invite).
If you use the module files in this repository for your analysis please you can cite the nf-core publication as follows:
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.
We are using self-hosted runners for the CI tests, managed via RunsOn.