Merge pull request #1002 from nf-core/mpcdf-specify-apptainer-versions

MPCDF clusters: specify apptainer version

Author: jfy133

conf/mpcdf.config

@@ -16,7 +16,7 @@ profiles {
                 cpus: 72,
                 time: 24.h
             ]
-            beforeScript = 'module load singularity'
+            beforeScript = 'module load apptainer/1.4.3'
             executor     = 'slurm'
         }
 

conf/mpcdf_viper.config

@@ -12,7 +12,7 @@ process {
         cpus: 256,
         time: 24.h
     ]
-    beforeScript   = 'module load apptainer'
+    beforeScript   = 'module load apptainer/1.4.3'
     clusterOptions = '--export=ALL'
     executor       = 'slurm'
 }

docs/mpcdf.md

@@ -10,7 +10,9 @@ Currently profiles for the following clusters are supported: `raven`.
 
 For `viper`, please see the `mpcdf_viper` profile in the [MPCDF Viper Configuration](viper.md).
 
-All profiles use `singularity` as the corresponding containerEngine. To prevent repeatedly downloading the same singularity image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_SINGULARITY_CACHEDIR` bash variable.
+All profiles use `apptainer/1.4.3` as the corresponding containerEngine.
+Make sure to `module load apptainer/1.4.3` in the environent where you execute `nextflow run`.
+To prevent repeatedly downloading the same singularity image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_SINGULARITY_CACHEDIR` bash variable.
 
 > NB: Nextflow will need to submit the jobs via SLURM to the clusters and as such the commands above will have to be executed on one of the head nodes. Check the [MPCDF documentation](https://www.mpcdf.mpg.de/services/computing).
 

docs/mpcdf_viper.md

@@ -8,7 +8,8 @@ To run Nextflow, the `jdk` and `apptainer` modules must be loaded.
 
 This `mpcdf_viper` config is for `viper`. For `raven` see the [`mpcdf`](mpcdf.md) profile.
 
-All profiles use `apptainer` as the corresponding containerEngine.
+All profiles use `apptainer/1.4.3` as the corresponding containerEngine.
+Make sure to `module load apptainer/1.4.3` in the environment where you execute `nextflow run`.
 To prevent repeatedly downloading the same apptainer image for every pipeline run, for all profiles we recommend specifying a cache location in your `~/.bash_profile` with the `$NXF_APPTAINER_CACHEDIR` bash variable.
 
 > [!TIP]