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Alexander Peltzer 2022-03-07 13:44:00 +01:00 committed by GitHub
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@ -5,7 +5,7 @@ Configuration file to run nf-core pipelines on the cluster of the [Functional Ge
Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines. Note that, at present, this config has only been tested with nf-core/viralrecon, but should function similarly for other nf-core pipelines.
To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node. To use, run the pipeline with `-profile fgcz`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the FGCZ cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.
The config places your singularity cashe in your home directory for access by other projects your run in other working directories. The config places the singularity cache in your /srv/GT/ directory for access by all projects.
Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz Example: /usr/local/ngseq/src/nextflow/nextflow run -profile fgcz