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34 lines
1.6 KiB
Markdown
34 lines
1.6 KiB
Markdown
# nf-core/configs: PROFILE Configuration
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All nf-core pipelines have been successfully configured for use on the DANGPU at the
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Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen.
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To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU.
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## Modules
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Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. You can do this by issuing the commands below:
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```bash
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## Load Nextflow and Singularity environment modules
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module purge
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module load openjdk/11.0.0 nextflow/22.04.3 singularity/3.8.0
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# alternative module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0
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export NXF_OPTS='-Xms1g -Xmx4g'
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export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
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export NXF_TEMP=/scratch/tmp
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NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
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```
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create nextflow directories if they dont exist:
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```
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mkdir $NXF_SINGULARITY_CACHEDIR
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mkdir $NXF_HOME
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```
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Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm as resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
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```
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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```
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