Adding the MRC LMS Jex cluster

.github/workflows/main.yml

@@ -81,6 +81,7 @@ jobs:
           - "ipop_up"
           - "janelia"
           - "jax"
+          - "jex"
           - "ku_sund_dangpu"
           - "leicester"
           - "lugh"

README.md

@@ -138,6 +138,7 @@ Currently documentation is available for the following systems:
 - [iPOP-UP](docs/ipop_up.md)
 - [Janelia Research Campus](docs/janelia.md)
 - [JAX](docs/jax.md)
+- [Jex](docs/jex.md)
 - [KU SUND DANGPU](docs/ku_sund_dangpu.md)
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)

conf/jex.config

@@ -0,0 +1,32 @@
+params {
+  config_profile_name = 'Jex'
+  config_profile_description = 'Nextflow config file for the MRC LMS Jex cluster'
+  config_profile_contact = 'George Young (@A-N-Other)'
+  config_profile_url = 'https://lms.mrc.ac.uk/research-facility/bioinformatics-facility/'
+}
+
+process {
+  executor = 'slurm'
+  queue = {
+    if ( task.time <= 6.h && task.cpus <= 8 && task.memory <= 64.GB ) {
+      'nice'
+    } else if ( task.memory > 256.GB ) {
+      'hmem'
+    } else {
+      'cpu'
+    }
+  }
+  clusterOptions = '--qos qos_batch'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  cacheDir = '/opt/resources/apps/singularity/cache'
+}
+
+params {
+  max_memory = 4000.GB
+  max_cpus = 16
+  max_time = 3.d
+}

docs/jex.md

@@ -0,0 +1,39 @@
+# nf-core/configs: Configuration for the MRC LMS Jex cluster
+
+All `nf-core` pipelines have been configured for use on the
+[MRC LMS](https://lms.mrc.ac.uk/) Jex cluster and can be used by running with
+`-profile jex`.
+
+The [`jex.config`](../conf/jex.config) file has been customised to suit the
+cluster's SLURM system and streamlines the use of containerised `nf-core` workflows.
+Using this profile, `docker` images containing the required software will be downloaded
+and converted to `singularity` images prior to execution and jobs will be submitted
+to the correct SLURM partitions and QoS groups. Converted `singularity` images are
+cached in a central area to reduce duplication.
+
+To run a pipeline, `nextflow` and `singularity` will need to be loaded into your
+environment:
+
+```bash
+#
+# NOTE:
+# We use `module reset` rather than `module purge`, as Jex makes use of various
+# default modules that provide a consistent user environment.
+#
+
+module reset
+
+module load nextflow
+module load singularityce
+```
+
+Full documentation on now to run `nextflow` on Jex can be found on the internal
+[wiki](http://hpcwiki.lms.mrc.ac.uk). Remember:
+
+> Jex provides a special SLURM partition for running workflow managers, including
+> `nextflow`. Manager processes submitted with `--partition ctrl --qos qos_ctrl`
+> have elevated priorities and wallclock limits of up to 30 days.
+
+> Jex makes available various shared genome resources to avoid duplication.
+> These are located within `/opt/resources` and can be searched and referenced using
+> the `asset` command.

nfcore_custom.config

@@ -63,6 +63,7 @@ profiles {
     ipop_up          { includeConfig "${params.custom_config_base}/conf/ipop_up.config" }
     janelia          { includeConfig "${params.custom_config_base}/conf/janelia.config" }
     jax              { includeConfig "${params.custom_config_base}/conf/jax.config" }
+    jex              { includeConfig "${params.custom_config_base}/conf/jex.config" }
     ku_sund_dangpu   { includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
     leicester        { includeConfig "${params.custom_config_base}/conf/leicester.config" }
     lugh             { includeConfig "${params.custom_config_base}/conf/lugh.config" }