Add disk labels (#390)

* Add disk labels * Set disk label denoising * set disk storage to memory * remove disk label * refactor config * Update src/wf_utils/labels_tw.config --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
openproblems-bio · Mar 13, 2024 · ee79ec8 · ee79ec8
1 parent 2201492
commit ee79ec8
Show file tree

Hide file tree

Showing 4 changed files with 19 additions and 6 deletions.
diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml
@@ -40,4 +40,4 @@ platforms:
         github: KlugerLab/ALRA
   - type: nextflow
     directives: 
-      label: [ "midtime", highmem, highcpu ]
+      label: [ midtime, highmem, highcpu]
diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml
@@ -38,4 +38,4 @@ platforms:
           - scottgigante-immunai/knn-smoothing@python_package
   - type: nextflow
     directives: 
-      label: [ "midtime", highmem, highcpu ]
+      label: [ midtime, highmem, highcpu ]
diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml
@@ -38,4 +38,4 @@ platforms:
         bioc: [ SingleCellExperiment, NewWave ]
   - type: nextflow
     directives:
-      label: [ "midtime", highmem, highcpu ]
+      label: [ midtime, highmem, highcpu ]
diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config
@@ -1,6 +1,9 @@
 process {
   executor = 'awsbatch'
 
+  // Default disk space
+  disk = 50.GB
+
   // Retry for exit codes that have something to do with memory issues
   errorStrategy = { task.attempt < 3 && task.exitStatus in ((130..145) + 104) ? 'retry' : 'ignore' }
   maxRetries = 3
@@ -11,9 +14,19 @@ process {
   withLabel: midcpu { cpus = 15 }
   withLabel: highcpu { cpus = 30 }
 
-  withLabel: lowmem { memory = { get_memory( 20.GB * task.attempt ) } }
-  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
-  withLabel: highmem { memory = { get_memory( 100.GB * task.attempt ) } }
+  withLabel: lowmem { 
+    memory = { get_memory( 20.GB * task.attempt ) } 
+    disk = { 50.GB * task.attempt } 
+  }
+  withLabel: midmem { 
+    memory = { get_memory( 50.GB * task.attempt ) }
+    disk = { 100.GB * task.attempt } 
+  }
+  withLabel: highmem {
+    memory = { get_memory( 100.GB * task.attempt ) }
+    disk = { 200.GB * task.attempt } 
+  }
+
 }
 
 def get_memory(to_compare) {