nf-core/configs: seattlechildrens
The SCRI (seattle childrens research institute) cluster profile
Seattle Children’s Research Institute Configuration
All nf-core pipelines have been successfully configured for use on the the Sasquatch HPC at Seattle Children Research Institude (SCRI), Seattle, WA.
To use, run the pipeline with -profile seattlechildrens. This will download and launch the pipeline using seattlechildrens.config which has been pre-configured with a setup suitable for the Sasquatch cluster at SCRI.
This profile assumes that you will use the cpu-core-sponsored partition. If you need to use gpu-core-sponsored for some steps, you can get in touch with Research Scientific Computing on Teams or email about how to modify the pipeline.
We also maintain a webpage about Nextflow within the Seattle Children’s intranet.
Project info
This config file is created for the use on the Sasquatch HPC at Seattle Children Research Institude (SCRI), Seattle, WA. Using this config will pre-configure a set up suitable for the Sasquatch HPC. The Singularity images will be downloaded to run on the cluster. The nextflow pipeline should be executed inside of the Sasquatch system.
Below are mandatory information SCRI
Before running the pipeline you will need to create a Nextflow environment on mamba. Singularity is on the path by default and does not need to be loaded.
Create a Nextflow mamba environment
- Create nextflow.yml file containing the following content. This YAML file can be utilized to set up a mamba environment, specifying both the version of Nextflow and the environment name.
name: nextflow
channels:
- bioconda
- conda-forge
dependencies:
- python>=3.9
- nextflow==24.10.4
- nf-core==3.2.0
- graphviz
- Setting channel priority
Make sure that channel priority is set to flexible using the following comments:
# print your current conda settings
mamba config --describe channel_priority
# set to flexible if not already done
mamba config --set channel_priority flexible
- Create the Nextflow
mambaenvironment
mamba env create -f nextflow.yaml
- Running in HPC (Sasquatch)
Please look into RSC-RP/nextflow_scri_config for details.
# activate enviornment
mamba activate nextflow
# To list all the accounts you are authorized on HPC. For example if you have an account cpu-mylab-sponsored, your association is "mylab".
sshare -o "Account,Partition%20"
# Set your association as an environmental variable
export ASSOC="your_association_name"
# example to run nextflow pipeline (please replace with your own association, module, and temp directory)
nextflow run \
[nf-core/module_name] \
-profile seattlechildrens \
-workDir /data/hps/assoc/private/mylab/user/mmouse/temp_rnaseq \
You can find more information about computational resources here. You have to be an employee of SCRI to access the link.
Config file
def assoc = System.getenv("ASSOC") // Association belonging to a lab or project
//global parameters
params {
config_profile_description = 'The SCRI (seattle childrens research institute) cluster profile'
config_profile_contact = 'Research Scientific Computing (@RSC-RP)'
config_profile_url = 'https://github.com/RSC-RP/nextflow_scri_config'
}
//workDir = "/data/hps/assoc/private/${assoc}/user/$USER/temp"
process {
executor = 'slurm'
queue = 'cpu-core-sponsored'
memory = 7500.MB
time = '72h'
clusterOptions = "--account cpu-${assoc}-sponsored"
}
docker {
enabled = false
}
singularity {
enabled = true
autoMounts = true
cacheDir = "/data/hps/assoc/private/${assoc}/container"
runOptions = '--containall --no-home'
}
executor {
queueSize = 2000
}
executor
contact
