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Corrected unc_lccc.md #795

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Nov 19, 2024
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Corrected unc_lccc.md #795

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Corrected unc_lccc.md
alanhoyle Nov 13, 2024
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[automated] Fix code linting
nf-core-bot Nov 14, 2024
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18 changes: 5 additions & 13 deletions docs/unc_lccc.md
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# nf-core/configs: PROFILE Configuration

All nf-core pipelines have been successfully configured for use on the Lineberger Bioinformatics Group cluster at the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center.
nf-core pipelines have been successfully configured for use on the Lineberger Bioinformatics Group cluster at the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center.

To use, run the pipeline with `-profile unc_lccc`. This will download and launch the [`unc_lccc.config`](../conf/unc_lccc.config) which has been pre-configured with a setup suitable for the LBG cluster. Using this profile, docker images containing all of the required software will be downloaded, and converted to a Singularity/Apptainer image before execution of the pipeline.
To use, run the pipeline with `-profile unc_lccc` in the `nextflow run [...]` command. This will download and launch the [`unc_lccc.config`](../conf/unc_lccc.config) which has been pre-configured with a setup suitable for the LBG cluster. Using this profile, Docker images containing all of the required software will be downloaded, and converted to a Apptainer/Singularity image during execution of the pipeline.

## Below are non-mandatory information e.g. on modules to load etc
## Below are non-mandatory information

Before running pipelines you will need to login to a compute node and install nextflow https://www.nextflow.io/. You can do this by issuing the commands below:
Before running pipelines you should login to a compute node and install `nextflow` into your home directory. Directions at the following link: https://www.nextflow.io/. There is a copy of the `nextflow` executable in our default setup, but it tends to lag behind the released versions, so may or may not work with a given workflow.

```bash
## install Nextflow
module purge
module load Nextflow/0.32.0
module load Singularity/2.6.0
```

> NB: You will need an account to use the in order to run the pipelines. If in doubt contact <[email protected]>.
> NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
> NB: You will need an account to use the in order to run the pipelines and the `nextflow` commands will need to run on compute nodes, not a login node. If in doubt contact <[email protected]>.
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