From 1d5ceb6a0ba133fd4f31c457e44a8aa4f58318ae Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 29 Nov 2018 17:49:03 +0000 Subject: [PATCH] Minor modifications --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 770a3ec..c5ed49f 100644 --- a/README.md +++ b/README.md @@ -18,13 +18,13 @@ A repository for hosting nextflow config files containing custom parameters requ ## Using an existing config -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. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. +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. ### 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. +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 scope`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) to your config file. Similarly, you can add and customise 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 available to 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/configs`](https://github.com/nf-core/configs/tree/master/conf). @@ -34,7 +34,7 @@ If you want to use an existing config available in `nf-core/configs`, and you're ## Adding a new config -If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all `nf-core` pipelines, and to everyone within your organisation. You will simply have to specify `-profile ` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. +If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile ` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. ### Testing @@ -57,7 +57,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs 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/configs` 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. +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. ## Help