Merge pull request #562 from cruk-mi/crukmi-change

Some changes regarding definition of software versions
nf-core · Oct 3, 2023 · b19f3c2 · b19f3c2
2 parents af37a64 + 4491908
commit b19f3c2
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diff --git a/conf/crukmi.config b/conf/crukmi.config
@@ -12,7 +12,7 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load apps/apptainer/1.2.0'
+  beforeScript = 'module load apps/apptainer'
   executor     = 'slurm'
   queue        = { task.memory <= 240.GB ? 'compute' : 'hmem' }
 

diff --git a/docs/crukmi.md b/docs/crukmi.md
@@ -2,14 +2,14 @@
 
 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 griffin HPC. Using this profile, singularity images will be downloaded to run on the cluster and stored in a centralised location.
+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, Apptainer/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 environment modules
 module purge
-module load apps/nextflow/22.04.5
+module load apps/nextflow
 ```
 
 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.