https://github.com/cnr-ibba/nf-modules
Custom Nextflow DSL2 modules
https://github.com/cnr-ibba/nf-modules
dsl2 modules nextflow nextflow-modules
Last synced: 3 months ago
JSON representation
Custom Nextflow DSL2 modules
- Host: GitHub
- URL: https://github.com/cnr-ibba/nf-modules
- Owner: cnr-ibba
- License: mit
- Created: 2021-05-28T15:02:03.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2025-11-14T11:35:34.000Z (7 months ago)
- Last Synced: 2025-11-14T13:21:15.620Z (7 months ago)
- Topics: dsl2, modules, nextflow, nextflow-modules
- Language: Nextflow
- Homepage:
- Size: 322 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# cnr-ibba/nf-modules
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
A repository for hosting custom [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
modules not hosted in [nf-core/modules](https://github.com/nf-core/modules)
with process definitions and their associated documentation.
## Table of contents
- [cnr-ibba/nf-modules](#cnr-ibbanf-modules)
- [Table of contents](#table-of-contents)
- [Using existing modules](#using-existing-modules)
- [Adding new modules](#adding-new-modules)
- [Acknowledgment](#acknowledgment)
## Using existing modules
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/`](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.
1. Install the latest version of [`nf-core/tools`](https://github.com/nf-core/tools#installation) (`>=2.10`)
2. List the available modules:
```console
$ nf-core modules --git-remote https://github.com/cnr-ibba/nf-modules.git list remote
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.dev0 - https://nf-co.re
INFO Modules available from https://github.com/cnr-ibba/nf-modules.git (master):
┏━━━━━━━━━━━━━━━━━━━━┓
┃ Module Name ┃
┡━━━━━━━━━━━━━━━━━━━━┩
│ bamaddrg │
│ bamtools/coverage │
│ freebayes/chunk │
│ freebayes/multi │
│ freebayes/single │
│ freebayes/splitbam │
│ seqkit/rmdup │
└────────────────────┘
```
3. Install the module in your pipeline directory:
```console
$ nf-core modules --git-remote https://github.com/cnr-ibba/nf-modules.git install freebayes/splitbam
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.dev0 - https://nf-co.re
INFO Installing 'freebayes/splitbam'
INFO Use the following statement to include this module:
include { FREEBAYES_SPLITBAM } from '../modules/cnr-ibba/freebayes/splitbam/main'
```
4. Import the module in your Nextflow script (fix the path accordingly your
project):
```nextflow
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FREEBAYES_SPLITBAM } from './modules/cnr-ibba/freebayes/splitbam/main'
```
5. Remove the module from the pipeline repository if required:
```console
$ nf-core modules --git-remote https://github.com/cnr-ibba/nf-modules.git remove freebayes/splitbam
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.dev0 - https://nf-co.re
INFO Removed files for 'freebayes/splitbam' and its dependencies 'freebayes/splitbam'.
```
6. Check that a locally installed nf-core module is up-to-date compared to the one hosted in this repo:
```console
$ nf-core modules --git-remote https://github.com/cnr-ibba/nf-modules.git lint freebayes/splitbam
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.dev0 - https://nf-co.re
INFO Linting pipeline: '.'
INFO Linting module: 'freebayes/splitbam'
INFO Found 6 inputs in modules/cnr-ibba/freebayes/splitbam/main.nf
INFO Found 3 outputs in modules/cnr-ibba/freebayes/splitbam/main.nf
╭─ [!] 4 Module Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Module name │ File path │ Test message │
│╶────────────────────┼──────────────────────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────╴│
│ freebayes/splitbam │ modules/cnr-ibba/freebayes/splitbam/main.nf │ Conda update: bioconda::freebayes 1.3.6 -> 1.3.7 │
│ freebayes/splitbam │ modules/cnr-ibba/freebayes/splitbam/main.nf │ Unable to connect to container registry, code: 403, url: │
│ │ │ https://www.docker.com/bunop/freebayes:v0.1 │
│ freebayes/splitbam │ modules/cnr-ibba/freebayes/splitbam/main.nf │ Container versions do not match │
│ freebayes/splitbam │ modules/cnr-ibba/freebayes/splitbam/meta.yml │ meta is present as an output in meta.yml but not in main.nf │
│ ╵ ╵ │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 44 Tests Passed │
│ [!] 4 Test Warnings │
│ [✗] 0 Tests Failed │
╰───────────────────────╯
```
## Adding new modules
If you wish to contribute a new module, cosider to contribute to the original
[nf-core/modules](https://github.com/nf-core/modules) instead. Please see the
documentation on the
[nf-core website](https://nf-co.re/developers/modules#writing-a-new-module-reference).
## Acknowledgment
This pipeline uses code and infrastructure developed and maintained by the
[nf-core](https://nf-co.re) community, reused here under the
[MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
> 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.
> In addition, references of tools and data used in this pipeline are as follows: