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Merge pull request #17 from ewels/master
Added support for new params.custom_config_base option
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2 changed files with 26 additions and 3 deletions
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README.md
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README.md
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@ -28,7 +28,30 @@ 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. You can then run the pipeline with the `-c` parameter - see [Testing](#testing) for example.
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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. Then run the pipeline with `--custom_config_base`
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or `params.custom_config_base` set to the location of the directory containing the repository files:
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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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```
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Alternatively, instead of using the configuration profiles from this repository, you can run your
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pipeline directly calling the single institutional config file that you need with the `-c` parameter.
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```bash
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## Example command for nf-core/rnaseq
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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
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> files + singularity containers + institutional configs in one go for you, to make this process easier.
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## Adding a new config
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@ -8,7 +8,7 @@
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* name here.
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*/
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config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/conf"
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config_base = "${params.custom_config_base}/conf"
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profiles {
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binac { includeConfig "${config_base}/binac.config" }
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