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Merge pull request #419 from AdrijaK/master
add config for KU_SUND_DANGPU
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1
.github/workflows/main.yml
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1
.github/workflows/main.yml
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@ -67,6 +67,7 @@ jobs:
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- "ifb_core"
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- "imperial"
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- "jax"
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- "ku_sund_dangpu"
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- "lugh"
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- "marvin"
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- "medair"
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@ -122,6 +122,7 @@ Currently documentation is available for the following systems:
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- [ICR_DAVROS](docs/icr_davros.md)
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- [IMPERIAL](docs/imperial.md)
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- [JAX](docs/jax.md)
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- [KU SUND DANGPU](docs/ku_sund_dangpu.md)
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- [LUGH](docs/lugh.md)
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- [MAESTRO](docs/maestro.md)
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- [MARVIN](docs/marvin.md)
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25
conf/ku_sund_dangpu.config
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conf/ku_sund_dangpu.config
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params {
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config_profile_contact = 'Adrija Kalvisa <adrija.kalvisa@sund.ku.dk>'
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config_profile_description = 'dangpufl01 configuration'
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config_profile_url = ''
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// General cpus/memory/time requirements
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max_cpus = 30
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max_memory = 200.GB
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max_time = 72.h
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}
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process {
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executor = 'slurm'
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}
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executor {
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queueSize = 5
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}
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singularity {
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enabled = true
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autoMounts = true
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runOptions = '--bind /projects:/projects'
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}
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docs/ku_sund_dangpu.md
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docs/ku_sund_dangpu.md
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# nf-core/configs: ku_sund_dangpu 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 java/11.0.15 nextflow/22.04.4 singularity/3.8.0
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# alternative modules for older nextflow version (v.21) that works with java 8:
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# 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/${USER}/cache/nxf-home
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export NXF_TEMP=/scratch/tmp
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export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
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```
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Create the user-specific nextflow directories if they don't exist yet:
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```
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mkdir $NXF_SINGULARITY_CACHEDIR
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mkdir $NXF_HOME
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```
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Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
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```
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nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
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```
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@ -49,6 +49,7 @@ profiles {
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ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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jax { includeConfig "${params.custom_config_base}/conf/jax.config" }
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ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
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lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" }
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maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" }
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marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" }
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