Merge pull request #517 from SPPearce/crukmi

Update CRUKMI config
nf-core · Jun 29, 2023 · 3248fa4 · 3248fa4
2 parents 02a93a4 + f817111
commit 3248fa4
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Showing 4 changed files with 11 additions and 30 deletions.
diff --git a/README.md b/README.md
@@ -245,7 +245,6 @@ Currently documentation is available for the following pipelines within specific
 - rnavar
   - [MUNIN](docs/pipeline/rnavar/munin.md)
 - sarek
-  - [Cancer Research UK Manchester Institute](docs/pipeline/sarek/crukmi.md)
   - [EVA](docs/pipeline/sarek/eva.md)
   - [MUNIN](docs/pipeline/sarek/munin.md)
   - [SBC_SHARC](docs/pipeline/sarek/sbc_sharc.md)

diff --git a/conf/crukmi.config b/conf/crukmi.config
@@ -12,8 +12,8 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load apps/singularity/3.8.0'
-  executor = 'pbs'
+  beforeScript = 'module load apps/apptainer/1.0.0'
+  executor = 'slurm'
 
   errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
   maxErrors = '-1'
@@ -35,20 +35,20 @@ process {
   }
 
   withLabel:process_high {
-    cpus = { check_max( 16 * task.attempt, 'cpus' ) }
-    memory = { check_max( 80.GB * task.attempt, 'memory' ) }
+    cpus = { check_max( 48 * task.attempt, 'cpus' ) }
+    memory = { check_max( 256.GB * task.attempt, 'memory' ) }
   }
 
 }
 
 executor {
-    name = 'pbs'
+    name = 'slurm'
     queueSize = 1000
     pollInterval = '10 sec'
 }
 
 params {
-  max_memory = 2000.GB
-  max_cpus = 32
+  max_memory = 4000.GB
+  max_cpus = 96
   max_time = 72.h
 }
diff --git a/conf/pipeline/sarek/crukmi.config b/conf/pipeline/sarek/crukmi.config
diff --git a/docs/crukmi.md b/docs/crukmi.md
@@ -1,15 +1,15 @@
 # nf-core/configs: Cancer Research UK Manchester Institute Configuration
 
-All nf-core pipelines have been successfully configured for the use on the HPC (phoenix) at Cancer Research UK Manchester Institute.
+All nf-core pipelines have been successfully configured for the use on the HPC (griffin) at Cancer Research UK Manchester Institute.
 
-To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the phoenix HPC. Using this profile, singularity images will be downloaded to run on the cluster.
+To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the griffin HPC. Using this profile, singularity images will be downloaded to run on the cluster and stored in a centralised location.
 
 Before running the pipeline you will need to load Nextflow using the environment module system, for example via:
 
 ```bash
-## Load Nextflow and Singularity environment modules
+## Load Nextflow environment modules
 module purge
 module load apps/nextflow/22.04.5
 ```
 
-The pipeline should always be executed inside a workspace on the `/scratch/` system. All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory.
+The pipeline should always be executed inside a workspace on the `/scratch/` system. All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large.