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Merge pull request #230 from nf-core/docs-custom_config_base

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Phil Ewels 2021-08-23 19:34:30 +02:00 committed by GitHub
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@ -39,27 +39,23 @@ You should be able to get a good idea as to how other people are customising the
### Offline usage ### 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. To use nf-core pipelines offline, we recommend using the `nf-core download` helper tool. This will download both the pipeline files and also the config profiles from `nf-core/configs`. The pipeline files are then edited to load the configs from their relative file path correctly.
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 ```bash
## Download and unzip the config files # Download the workflow + transfer to offline cluster
cd /path/to/my/configs nf-core download rnaseq
wget https://github.com/nf-core/configs/archive/master.zip scp nf-core-rnaseq-3.0.tar.gz me@myserver.com:/path/to/workflows # or however you prefer to transfer files to your offline cluster
unzip master.zip # Connect to offline cluster
ssh me@myserver.com
## Run the pipeline # Extract workflow files
cd /path/to/my/data cd /path/to/workflows
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/ tar -xzf nf-core-rnaseq-3.0.tar.gz
# Run workflow
cd /path/to/data
nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile mycluster
``` ```
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. If required, you can instead download the nf-core/configs files yourself and customise the `--custom_config_base` / `params.custom_config_base` parameter in each pipeline to to set to the location of the configs directory.
```bash
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 ## Adding a new config