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Don't recommend setting --custom_config_base manually
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README.md
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README.md
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@ -39,27 +39,22 @@ You should be able to get a good idea as to how other people are customising the
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### Offline usage
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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.
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Then run the pipeline with `--custom_config_base` or `params.custom_config_base` set to the location of the directory containing the repository files:
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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.
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```bash
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## Download and unzip the config files
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cd /path/to/my/configs
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wget https://github.com/nf-core/configs/archive/master.zip
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unzip master.zip
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## Run the pipeline
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cd /path/to/my/data
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nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
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# Download the workflow + transfer to offline cluster
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nf-core download rnaseq
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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
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ssh me@myserver.com
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# Extract workflow files
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cd /path/to/workflows
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tar -xzf nf-core-rnaseq-3.0.tar.gz
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# Run workflow
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cd /path/to/data
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nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile mycluster
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```
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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.
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```bash
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nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
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```
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> 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.
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If you prefer, you can download these config profiles 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.
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## Adding a new config
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