[WIP] Add the Brain Image Library (BIL) cluster profile

.github/CODEOWNERS

@@ -5,3 +5,4 @@
 **/utd_ganymede** @edmundmiller @alyssa-ab
 **/unsw_katana** @jscgh
 **/seadragon** @jiawku
+**/brain** @icaoberg

.github/workflows/main.yml

@@ -50,6 +50,7 @@ jobs:
           - "biohpc_gen"
           - "biowulf"
           - "bluebear"
+          - "brain"
           - "cambridge"
           - "cannon"
           - "cbe"

README.md

@@ -103,6 +103,7 @@ Currently documentation is available for the following systems:
 - [BIOHPC_GEN](docs/biohpc_gen.md)
 - [BIOWULF](docs/biowulf.md)
 - [BLUEBEAR](docs/bluebear.md)
+- [BRAIN](docs/brain.md)
 - [CAMBRIDGE](docs/cambridge.md)
 - [CANNON](docs/cannon.md)
 - [CBE](docs/cbe.md)

conf/brain.config

@@ -0,0 +1,72 @@
+// ─────────────────────────────────────────────────────────────────────────────
+// Global Parameters
+// ─────────────────────────────────────────────────────────────────────────────
+params {
+    config_profile_name        = 'Brain Image Library Analysis Ecosystem'
+    config_profile_description = 'A public resource enabling researchers to deposit, analyze, mine, share, and interact with large brain image datasets.'
+    config_profile_url         = 'https://www.brainimagelibrary.org'
+    config_profile_contact     = 'Ivan Cao-Berg (@icaoberg)'
+
+    // General resource boundaries (used in profile as well)
+    max_memory = 2.9.Tb
+    max_cpus   = 80
+    max_time   = 48.h
+
+    // Ignore iGenomes when not needed
+    igenomes_ignore = true
+    igenomesIgnore  = true
+}
+
+// ─────────────────────────────────────────────────────────────────────────────
+// Singularity Configuration
+// ─────────────────────────────────────────────────────────────────────────────
+singularity {
+    enabled     = true
+    autoMounts  = true
+    runOptions  = '''
+        --home $HOME:/bil/users/$USER \
+        --bind /scratch \
+        --bind /local
+    '''
+}
+
+// ─────────────────────────────────────────────────────────────────────────────
+// Executor Configuration
+// ─────────────────────────────────────────────────────────────────────────────
+executor {
+    queueSize       = 10
+    submitRateLimit = '5 sec'
+}
+
+// ─────────────────────────────────────────────────────────────────────────────
+// Profiles
+// ─────────────────────────────────────────────────────────────────────────────
+profiles {
+    compute {
+        params {
+            config_profile_name        = 'BIL - General Computing Partition'
+            config_profile_description = 'Brain Image Library Analysis Ecosystem at the Pittsburgh Supercomputing Center'
+            config_profile_url         = 'https://www.brainimagelibrary.org'
+            config_profile_contact     = 'Ivan Cao-Berg (@icaoberg)'
+        }
+
+        process {
+            executor        = 'slurm'
+            queue           = 'compute'
+            queueSize       = 10
+            clusterOptions  = '--qos=normal'
+
+            // Set scratch directory to /local
+            scratch        = true
+            scratchMount   = '/local'
+
+            // Default per-process limits
+            resourceLimits = [
+                memory: 128.Gb,
+                cpus  : 16,
+                time  : 4.h
+            ]
+        }
+    }
+}
+

docs/brain.md

@@ -0,0 +1,25 @@
+# nf-core/configs: Brain Image Library Analysis Ecosystem Configuration
+
+All nf-core pipelines have been successfully configured for use on the Brain Image Libraryy (BIL) cluster at the Pittsburgh Supercomputing Center.
+
+To use, run the pipeline with `-profile brain`. This will download and launch the [`brain.config`](../conf/brain.config) which has been pre-configured with a setup suitable for the Brain Image Library (BIL) Analysis Ecosystem. 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 Brain Image Library (BIL) Analysis Ecosystem
+
+Nextflow is not installed by default on the Brain Image Library Analysis Ecosystem.
+
+- 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 shouldin't run directly on a login node but on a compute node.
+
+1. Run nextflow on a compute node with submit host capability:
+
+```bash
+# Run nextflow workflow
+nextflow run \\
+nf-core/chipseq \\
+-resume \\
+-profile test,brain
+```

nfcore_custom.config

@@ -58,6 +58,9 @@ profiles {
     bluebear {
         includeConfig "${params.custom_config_base}/conf/bluebear.config"
     }
+    brain {
+        includeConfig "${params.custom_config_base}/conf/brain.config"
+    }
     cambridge {
         includeConfig "${params.custom_config_base}/conf/cambridge.config"
     }