mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
175 lines
9.1 KiB
Markdown
175 lines
9.1 KiB
Markdown
# 
|
|
|
|
[](https://www.nextflow.io/)
|
|
[](https://docs.conda.io/en/latest/)
|
|
[](https://www.docker.com/)
|
|
[](https://sylabs.io/docs/)
|
|
|
|
|
|
[](https://nfcore.slack.com/channels/modules)
|
|
|
|
[](https://twitter.com/nf_core)
|
|
[](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
|
|
|
|
,--./,-.
|
|
___ __ __ __ ___ /,-._.--~\
|
|
|\ | |__ __ / ` / \ |__) |__ } {
|
|
| \| | \__, \__/ | \ |___ \`-._,-`-,
|
|
`._,._,'
|
|
|
|
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/adding_modules).
|
|
|
|
> 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).
|
|
|
|
<!---
|
|
|
|
### Offline usage
|
|
|
|
If you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information:
|
|
|
|
```bash
|
|
include /path/to/downloaded/modules/directory/
|
|
```
|
|
|
|
Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:
|
|
|
|
```bash
|
|
nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
|
|
```
|
|
|
|
> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
|
|
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
|
|
|
|
# New test data created for the module- sequenzautils/bam2seqz
|
|
The new test data is an output from another module- sequenzautils/bcwiggle- (which uses sarscov2 genome fasta file as an input).
|
|
-->
|