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Merge pull request #17 from ewels/master

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Added support for new params.custom_config_base option
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Phil Ewels 2019-03-05 16:56:13 +01:00 committed by GitHub
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README.md
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@ -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 unzip 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` 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

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nfcore_custom.config
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@ -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" }