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Added instructions for module loading

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Rogan Grant 2021-07-28 18:11:10 -05:00
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docs/nu_genomics.md
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# nf-core/configs: NU_Genomics Configuration # nf-core/configs: NU_Genomics Configuration
All nf-core pipelines have been successfully configured for use on the Quest Genomics Nodes at Northwestern University. All nf-core pipelines have been successfully configured for use on the Quest Genomics Nodes at Northwestern University. Note that, at present, this config has only been tested with nf-core/RNA-seq, but should function similarly for other nf-core pipelines. If you would like to test other pipelines and share on the genomics-rcs Slack, we would be very much obliged.
To use, run the pipeline with `-profile nu_genomics`. This will download and launch the [`nu_genomics.config`](../conf/nu_genomics.config) which has been pre-configured with a setup suitable for the Quest Genomics Nodes. 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. To use, run the pipeline with `-profile nu_genomics`. This will download and launch the [`nu_genomics.config`](../conf/nu_genomics.config) which has been pre-configured with a setup suitable for the Quest Genomics Nodes. 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.
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curl -s https://github.com/nextflow-io/nextflow/releases/download/v20.11.0-edge/nextflow-20.11.0-edge-all | bash curl -s https://github.com/nextflow-io/nextflow/releases/download/v20.11.0-edge/nextflow-20.11.0-edge-all | bash
``` ```
Note that while the config does explicitly load the necessary modules, you will often need to load them manually anyway. Please do so before each run as follows, or you may run into errors:
```bash
module purge
module load singularity/latest
module load graphviz/2.40.1
```
## Use of iGenomes ## Use of iGenomes
A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. A local copy of the iGenomes resource with all commonly used genomes has been made available for all of Quest so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.