just use labels_tw (#448)

openproblems-bio · Apr 29, 2024 · 1a10195 · 1a10195
1 parent b6b85a3
commit 1a10195
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh
@@ -10,16 +10,6 @@ output_state: "$id/state.yaml"
 publish_dir: s3://openproblems-data/resources/predict_modality/datasets
 HERE
 
-cat > /tmp/nextflow.config << HERE
-process {
-  executor = 'awsbatch'
-  withName:'.*publishStatesProc' {
-    memory = '16GB'
-    disk = '100GB'
-  }
-}
-HERE
-
 tw launch https://github.com/openproblems-bio/openproblems-v2.git \
   --revision main_build \
   --pull-latest \
@@ -28,5 +18,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \
   --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
   --params-file /tmp/params.yaml \
   --entry-name auto \
-  --config /tmp/nextflow.config \
+  --config src/wf_utils/labels_tw.config \
   --labels predict_modality,process_datasets
diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config
@@ -39,6 +39,12 @@ process {
     containerOptions = { workflow.containerEngine == "singularity" ? '--nv':
        ( workflow.containerEngine == "docker" ? '--gpus all': null ) }
   }
+
+  // make sure publishstates gets enough disk space and memory
+  withName:'.*publishStatesProc' {
+    memory = '16GB'
+    disk = '100GB'
+  }
 }
 
 def get_memory(to_compare) {