millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Refine README

Browse source
This commit is contained in:
drpatelh 2019-07-26 13:30:26 +01:00
parent ef8c13a7d8
commit eb9aeea775
4 changed files with 22 additions and 32 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

48
README.md
View file

@ -16,68 +16,52 @@ A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl
## Using an existing module
The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation.
The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally.
You should be able to get a good idea as to how other people are using module files by looking at pipelines available in nf-core e.g. [`nf-core/rnaseq`](https://github.com/nf-core/rnaseq/pull/162)
### Configuration and parameters
The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all nf-core pipelines.
All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customise the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/modules`](https://github.com/nf-core/modules/tree/master/conf).
The module files hosted in this repository define a set of processes for software tools such as `fastc`, `trimgalore`, `bwa` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
### Offline usage
If you want to use an existing config available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline with `--custom_config_base`
or `params.custom_config_base` set to the location of the directory containing the repository files:
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
## Download and unzip the config files
cd /path/to/my/modules
wget https://github.com/nf-core/modules/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/modules/modules-master/
include /path/to/downloaded/modules/directory/
```
Alternatively, instead of using the configuration profiles from this repository, you can run your
pipeline directly calling the single institutional config file that you need with the `-c` parameter.
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/my/modules/modules-master/conf/my_config.config
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 modules in one go for you, to make this process easier.
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
## Adding a new config
## Adding a new module file
If you decide to upload your module file to `nf-core/module` then this will ensure that it will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within the community. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/modules`](https://github.com/nf-core/modules/tree/master/conf) for examples.
If you decide to upload your module file to `nf-core/modules` then this will ensure that it will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within the Nextflow community! See [`nf-core/modules`](https://github.com/nf-core/modules/tree/master/nf) for examples.
Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.
The definition and standards for module files is still under discussion amongst the community but hopefully, a description should be added here soon!
### Testing
If you want to add a new custom config file to `nf-core/modules` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter.
```bash
## Example command for nf-core/rnaseq
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'
```
If you want to add a new module config file to `nf-core/modules` please test that your pipeline of choice runs as expected by using the [`-include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement with a local version of the module file.
### Documentation
You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation. You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there.
You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the module file and extensive links to documentation for the tool(s) used in the module file. You can use the provided [`template.md`](docs/template.md) to guide you as to how to do this appropriately.
See [`nf-core/modules/docs`](https://github.com/nf-core/modules/tree/master/docs) for examples.
### Uploading to `nf-core/modules`
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`modules/`](https://github.com/nf-core/modules/tree/master/modules) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/modules/tree/master/docs) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively.
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`nf/`](https://github.com/nf-core/modules/tree/master/nf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/modules/tree/master/docs) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively.
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/modules` GitHub repo with the appropriate information.
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on `nf-core/modules` GitHub repo with the appropriate information.
We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.

2
docs/fastqc.md
View file

@ -0,0 +1,2 @@
# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!

2
docs/template.md Normal file
View file

@ -0,0 +1,2 @@
# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!

2
nf/fastqc.nf
View file

@ -0,0 +1,2 @@
# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!