https://github.com/amakunin/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Science Score: 13.0%
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary
Last synced: 9 months ago
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Repository
Repository to host tool-specific module files for the Nextflow DSL2 community!
Basic Info
- Host: GitHub
- Owner: amakunin
- License: mit
- Default Branch: master
- Homepage: https://nf-co.re
- Size: 138 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 0
Fork of nf-core/modules
Created about 3 years ago
· Last pushed about 3 years ago
https://github.com/amakunin/modules/blob/master/
# 
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
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[](https://sylabs.io/docs/)
[](https://nfcore.slack.com/channels/modules)
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[](https://www.youtube.com/c/nf-core)
> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
## Table of contents
- [Using existing modules](#using-existing-modules)
- [Adding new modules](#adding-new-modules)
- [Help](#help)
- [Citation](#citation)
## 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) (`>=2.0`)
2. List the available modules:
```console
$ nf-core modules list remote
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
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..
```
3. Install the module in your pipeline directory:
```console
$ nf-core modules install fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
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
```
4. Import the module in your Nextflow script:
```nextflow
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FASTQC } from './modules/nf-core/modules/fastqc/main'
```
5. Remove the module from the pipeline repository if required:
```console
$ nf-core modules remove fastqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.0
INFO Removing fastqc pipeline_modules.py:271
INFO Successfully removed fastqc pipeline_modules.py:285
```
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 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
```
## Adding new modules
If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/modules#writing-a-new-module-reference).
> Please be kind to our code reviewers and submit one pull request per module :)
## Help
For further information or help, don't hesitate to get in touch on [Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citation
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](https://dx.doi.org/10.1038/s41587-020-0439-x).
Owner
- Name: Alex Makunin
- Login: amakunin
- Kind: user
- Company: Wellcome Sanger Institute
- Repositories: 1
- Profile: https://github.com/amakunin