From 9fb5715c4ca0ef33c0227ddab697b0f0d0c4e575 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 5 Mar 2019 16:12:39 +0100 Subject: [PATCH 1/3] Added support for new params.custom_config_base option --- README.md | 27 +++++++++++++++++++++++++-- nfcore_custom.config | 2 +- 2 files changed, 26 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6d5b340..593e61b 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ 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. +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 @@ -28,7 +28,30 @@ You should be able to get a good idea as to how other people are customising the ### Offline usage -If you want to use an existing config available in `nf-core/configs`, 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. You can then run the pipeline with the `-c` parameter - see [Testing](#testing) for example. +If you want to use an existing config available in `nf-core/configs`, 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: + +```bash +## Download and unizp the config files +cd /path/to/my/configs +wget https://github.com/nf-core/configs/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/configs/configs-master/ +``` + +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. + +```bash +## Example command for nf-core/rnaseq +nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config .. +``` + +> Note that the nf-core/tools helper package has a `download` subcommand download required +> pipeline files for you to make this process easier. ## Adding a new config diff --git a/nfcore_custom.config b/nfcore_custom.config index 757b70b..2e4139c 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -8,7 +8,7 @@ * name here. */ -config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf" +config_base = "${params.custom_config_base}/conf" profiles { binac { includeConfig "${config_base}/binac.config" } From e0ba8e6f0794a571ca04d88f8828eac761770678 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 5 Mar 2019 16:28:10 +0100 Subject: [PATCH 2/3] Tweak the readme --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 593e61b..a50dc54 100644 --- a/README.md +++ b/README.md @@ -47,11 +47,11 @@ pipeline directly calling the single institutional config file that you need wit ```bash ## Example command for nf-core/rnaseq -nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config .. +nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config ``` -> Note that the nf-core/tools helper package has a `download` subcommand download required -> pipeline files for you to make this process easier. +> Note that the nf-core/tools helper package has a `download` command to download all required pipeline +> files + singularity containers + institutional configs in one go for you, to make this process easier. ## Adding a new config From d115909343f6f445902f27ca67fbedffc80fa8e6 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 5 Mar 2019 16:53:59 +0100 Subject: [PATCH 3/3] Tyop --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a50dc54..969a7ec 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ If you want to use an existing config available in `nf-core/configs`, and you're or `params.custom_config_base` set to the location of the directory containing the repository files: ```bash -## Download and unizp the config files +## Download and unzip the config files cd /path/to/my/configs wget https://github.com/nf-core/configs/archive/master.zip unzip master.zip