Merge pull request #701 from nf-core/dardel_java8_fix_and_apptainer_f…

…or_fuse

Dardel java8 fix and apptainer for fuse

conf/pdc_kth.config

@@ -76,14 +76,9 @@ singularity {
 
 process {
     // Should we lock these to specific versions?
-    beforeScript = 'module load PDC singularity'
+    beforeScript = 'module load PDC apptainer'
 
     executor = 'slurm'
     clusterOptions = { clusterOptionsCreator(task.memory, task.time, task.cpus) }
 }
 
-env {
-    // Handle java logging on stdout when discovering duplicated cgroups when
-    // running in singularity with Lustre mount
-    JAVA_TOOL_OPTIONS = "-Xlog:disable"
-}