Merge pull request #828 from KochInstitute-Bioinformatics/ki_luria

ki_luria

.github/workflows/main.yml

@@ -103,6 +103,7 @@ jobs:
           - "unsw_katana"
           - "ku_sund_danhead"
           - "kaust"
+          - "ki_luria"
           - "leicester"
           - "lugh"
           - "m3c"

README.md

@@ -155,6 +155,7 @@ Currently documentation is available for the following systems:
 - [UNSW_Katana](docs/unsw_katana.md)
 - [KU SUND DANHEAD](docs/ku_sund_danhead.md)
 - [KAUST](docs/kaust.md)
+- [KI_LURIA](docs/ki_luria.md)
 - [LUGH](docs/lugh.md)
 - [M3C](docs/m3c.md)
 - [MAESTRO](docs/maestro.md)

conf/ki_luria.config

@@ -0,0 +1,22 @@
+// Nextflow config for running on the Koch Institute of MIT Luria HPC cluster
+params {
+    config_profile_description = 'KI at MIT Luria HPC cluster profile.'
+    config_profile_contact     = 'Charlie Whittaker (@Charlie14557807)'
+    config_profile_url         = "https://igb.mit.edu/computing-resources/luria-cluster"
+}
+
+singularity {
+    enabled    = true
+    autoMounts = true
+}
+
+process {
+    resourceLimits = [
+        memory: 64.GB,
+        cpus: 16,
+        time: 12.h
+    ]
+    executor       = 'slurm'
+    clusterOptions = '-p normal'
+}
+

docs/ki_luria.md

@@ -0,0 +1,19 @@
+# nf-core/configs: KI at MIT Luria Configuration
+
+All nf-core pipelines have been successfully configured for use on the [KI at MIT Luria Cluster](https://igb.mit.edu/computing-resources/luria-cluster).
+
+To use, run the pipeline with `-profile ki_luria`. This will download and launch the [`ki_luria.config`](../conf/ki_luria.config) which has been pre-configured with a setup suitable for the Luria 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.
+
+## Below are non-mandatory information e.g. on modules to load etc
+
+Before running the pipeline you will need to activate the Nextflow conda environment and load Singularity using the environment module system on Luria Cluster. You can do this by issuing the commands below:
+
+```bash
+module add miniconda3/v4
+source /home/software/conda/miniconda3/bin/condainit
+conda activate /home/charliew/.conda/envs/nf-core_Oct24
+module add singularity/3.10.4
+```
+
+> NB: You will need an account to use the HPC cluster on Lura in order to run the pipeline.
+> 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.

nfcore_custom.config

@@ -217,6 +217,9 @@ profiles {
     kaust {
         includeConfig "${params.custom_config_base}/conf/kaust.config"
     }
+    ki_luria {
+        includeConfig "${params.custom_config_base}/conf/ki_luria.config"
+    }
     leicester {
         includeConfig "${params.custom_config_base}/conf/leicester.config"
     }