Merge pull request #486 from CarsonJM/uw_hyak_pedslabs

Added uw_hyak_pedslabs config

.github/workflows/main.yml

@@ -111,6 +111,7 @@ jobs:
           - "uppmax"
           - "utd_ganymede"
           - "utd_sysbio"
+          - "uw_hyak_pedslabs"
           - "uzh"
           - "vai"
           - "vsc_kul_uhasselt"

README.md

@@ -166,6 +166,7 @@ Currently documentation is available for the following systems:
 - [UPPMAX](docs/uppmax.md)
 - [UTD_GANYMEDE](docs/utd_ganymede.md)
 - [UTD_SYSBIO](docs/utd_sysbio.md)
+- [UW_HYAK_PEDSLABS](docs/uw_hyak_pedslabs.md)
 - [UZH](docs/uzh.md)
 - [VAI](docs/vai.md)
 - [VSC_KUL_UHASSELT](docs/vsc_kul_uhasselt.md)

conf/uw_hyak_pedslabs.config

@@ -0,0 +1,31 @@
+params {
+  config_profile_description = 'UW Hyak Pedslabs cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Carson J. Miller (@CarsonJM)'
+  config_profile_url = 'https://www.peds.uw.edu/'
+  max_memory = 742.GB
+  max_cpus = 40
+  max_time = 72.h
+}
+
+process {
+    executor = 'slurm'
+    queue = { task.attempt == 1 ? 'ckpt' : 'compute-hugemem' }
+    maxRetries = 1
+    clusterOptions = { "-A pedslabs" }
+    scratch = '/gscratch/scrubbed/pedslabs/'
+}
+
+executor {
+    queuesize = 50
+    submitRateLimit = '1 sec'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = '/gscratch/scrubbed/pedslabs/.apptainer'
+}
+
+debug {
+  cleanup = false
+}

docs/uw_hyak_pedslabs.md

@@ -0,0 +1,41 @@
+# University of Washington Hyak Profile for the Department of Pediatrics
+
+All nf-core pipelines have been successfully configured for use on the University of Washington's Hyak cluster, with this profile specific to the Department of Pediatrics partition.
+
+To use, run the pipeline with `-profile uw_hyak_pedslabs`. This will download and launch the [`uw_hyak_pedslabs.config`](../conf/uw_hyak_pedslabs.config) which has been pre-configured with a setup suitable for the Hyak cluster. 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.
+
+## Running the workflow on the Pasteur cluster
+
+Nextflow is not installed by default on Hyak.
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+Nextflow manages each process as a separate job that is submitted to the cluster by using the `sbatch` command.
+Nextflow shouldn't run directly on the submission node but on a compute node.
+
+To install and use Nextflow, the following process can be used:
+
+1. Install mamba and create a mamba environment containing nextflow and nf-core
+
+```bash
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
+bash Mambaforge-Linux-x86_64.sh -b -p $HOME/mambaforge
+mamba create -n nextflow -c bioconda -c conda-forge python=3.8 nf-core nextflow -y -q
+```
+
+2. Run nextflow on a compute node:
+
+```bash
+# create a screen
+screen -S nextflow
+# request a compute node (mem and time requests can be modified)
+salloc -A pedslabs -p compute-hugemem -N 1 -c 1 --mem=16GB --time=12:00:00
+# load the nextflow environment
+mamba activate nextflow
+# Run nextflow workflow
+nextflow run \\
+<nf-core-pipeline-name> \\
+-resume
+-profile uw_hyak_pedslabs \\
+--email <uw-net-id>@uw.edu
+```

nfcore_custom.config

@@ -93,6 +93,7 @@ profiles {
     uppmax           { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
     utd_ganymede     { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
     utd_sysbio       { includeConfig "${params.custom_config_base}/conf/utd_sysbio.config" }
+    uw_hyak_pedslabs { includeConfig "${params.custom_config_base}/conf/uw_hyak_pedslabs.config" }
     uzh              { includeConfig "${params.custom_config_base}/conf/uzh.config" }
     vai              { includeConfig "${params.custom_config_base}/conf/vai.config" }
     vsc_kul_uhasselt { includeConfig "${params.custom_config_base}/conf/vsc_kul_uhasselt.config" }