From 30c864e1121e5b5fcea5633eaa689498745670b2 Mon Sep 17 00:00:00 2001
From: Asaf Peer <Asaf.Peer@jax.org>
Date: Sun, 21 Mar 2021 06:49:11 -0400
Subject: [PATCH] added JAX conf

---
 conf/jax.config | 21 +++++++++++++++++++++
 docs/jax.md     |  8 ++++++++
 2 files changed, 29 insertions(+)
 create mode 100644 conf/jax.config
 create mode 100644 docs/jax.md

diff --git a/conf/jax.config b/conf/jax.config
new file mode 100644
index 0000000..a5437e9
--- /dev/null
+++ b/conf/jax.config
@@ -0,0 +1,21 @@
+params {
+      config_profile_description = 'The Jackson Laboratory Sumner HPC profile provided by nf-core/configs.'
+      config_profile_contact = 'Asaf Peer (@peera)'
+      config_profile_url = 'https://jacksonlaboratory.sharepoint.com/sites/ResearchIT/SitePages/Welcome-to-Sumner.aspx'
+    }
+
+executor.$slurm.queueSize = 250
+process {
+    executor = "slurm"
+    queue = "compute"
+    clusterOptions = {task.time < 72.h ? '-q batch' : '-q long'}
+    module = "slurm"
+    beforeScript = 'module load singularity'
+}
+singularity.enabled = true
+singularity.autoMounts = true
+params {
+      max_memory = 768.GB
+      max_cpus = 70
+      max_time = 336.h
+    }
diff --git a/docs/jax.md b/docs/jax.md
new file mode 100644
index 0000000..d38cfbe
--- /dev/null
+++ b/docs/jax.md
@@ -0,0 +1,8 @@
+# nf-core/configs: JAX Configuration
+
+All nf-core pipelines have been successfully configured for use on the JAX Sumner cluster at The Jackson Laboratory.
+
+To use, run the pipeline with `-profile jax`. This will download and launch the [`jax.config`](../conf/jax.config) which has been pre-configured with a setup suitable for JAX Sumner 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 and slurm will be used as well.
+
+>NB: You will need an account to use the HPC cluster JAX in order to run the pipeline. If in doubt contact IT.
+>NB: Nextflow should not be executed on the login nodes. If in doubt contact IT.