🧠 fix memory settings

kids-first · Sep 25, 2024 · d5bb923 · d5bb923
1 parent 417a4a1
commit d5bb923
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Showing 5 changed files with 10 additions and 6 deletions.
diff --git a/subworkflows/deepsomatic.cwl b/subworkflows/deepsomatic.cwl
@@ -231,6 +231,10 @@ steps:
               return MAKE_EXAMPLE_EA_MAP[self[1]];
             }
           }
+      ram:
+        source: model_type
+        valueFrom: |
+          $(self.search("PACBIO") != -1 ? 3 : null)
     out: [examples, candidates, gvcf]
   deepsomatic_call_variants:
     hints:

diff --git a/tools/deepsomatic_call_variants.cwl b/tools/deepsomatic_call_variants.cwl
@@ -6,7 +6,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: ResourceRequirement
-    ramMin: $(inputs.max_memory*1000)
+    ramMin: $(inputs.ram*1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
     dockerPull: 'google/deepsomatic:1.7.0-gpu'
@@ -34,7 +34,7 @@ inputs:
     doc: "Number of CPUs to allocate to this task."
   ram:
     type: 'int?'
-    default: 40
+    default: 32
     doc: "Maximum GB of RAM to allocate for this tool."
 outputs:
   output: 

diff --git a/tools/deepsomatic_make_examples.cwl b/tools/deepsomatic_make_examples.cwl
@@ -6,7 +6,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: ResourceRequirement
-    ramMin: $(inputs.max_memory*1000)
+    ramMin: $(inputs.ram*1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
     dockerPull: 'google/deepsomatic:1.7.0'
@@ -79,7 +79,7 @@ inputs:
     doc: "Number of CPUs to allocate to this task."
   ram:
     type: 'int?'
-    default: 1
+    default: 2
     doc: "Maximum GB of RAM to allocate for this tool."
 outputs:
   examples:

diff --git a/tools/deepsomatic_postprocess_variants.cwl b/tools/deepsomatic_postprocess_variants.cwl
@@ -6,7 +6,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: ResourceRequirement
-    ramMin: $(inputs.max_memory*1000)
+    ramMin: $(inputs.ram*1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
     dockerPull: 'google/deepsomatic:1.7.0-gpu'

diff --git a/tools/deepsomatic_vcf_stats_report.cwl b/tools/deepsomatic_vcf_stats_report.cwl
@@ -6,7 +6,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: ResourceRequirement
-    ramMin: $(inputs.max_memory*1000)
+    ramMin: $(inputs.ram*1000)
     coresMin: $(inputs.cpu)
   - class: DockerRequirement
     dockerPull: 'google/deepsomatic:1.7.0'