Various fixes (#4)

* fix compute env

* bump memory reqs

* use main openproblems repo

* update submodule

* bump labels

Author: rcannood

_viash.yaml

@@ -86,16 +86,10 @@ info:
       dest: resources_test/task_predict_modality
 
 repositories:
-  - name: openproblems_v2
+  - name: openproblems
     type: github
-    repo: openproblems-bio/openproblems-v2
+    repo: openproblems-bio/openproblems
     tag: main_build
-  - name: core
-    type: github
-    repo: openproblems-bio/core
-    # tag: build/main
-    tag: build/add_common_components
-    path: viash/core
 
 config_mods: |
   .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }

common

@@ -19,7 +19,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \
   --pull-latest \
   --main-script target/nextflow/workflows/process_datasets/main.nf \
   --workspace 53907369739130 \
-  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --compute-env 5DwwhQoBi0knMSGcwThnlF \
   --params-file /tmp/params.yaml \
   --entry-name auto \
   --config common/nextflow_helpers/labels_tw.config \

scripts/create_datasets/resources.sh

@@ -14,8 +14,8 @@ publish_dir="s3://openproblems-data/resources/task_predict_modality/results/${RU
 
 # write the parameters to file
 cat > /tmp/params.yaml << HERE
-input_states: s3://openproblems-data/resources/task_predict_modality/datasets/**/state.yaml
-rename_keys: 'input_train_mod1:output_train_mod1;input_train_mod2:output_train_mod2;input_test_mod1:output_test_mod1;input_test_mod2:output_test_mod2"
+input_states: "s3://openproblems-data/resources/task_predict_modality/datasets/**/state.yaml"
+rename_keys: "input_train_mod1:output_train_mod1;input_train_mod2:output_train_mod2;input_test_mod1:output_test_mod1;input_test_mod2:output_test_mod2"
 output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
@@ -25,7 +25,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \
   --workspace 53907369739130 \
-  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --compute-env 5DwwhQoBi0knMSGcwThnlF \
   --params-file /tmp/params.yaml \
   --entry-name auto \
   --config common/nextflow_helpers/labels_tw.config \

scripts/run_benchmark/run_full_seqeracloud.sh

@@ -34,7 +34,7 @@ tw launch https://github.com/openproblems-bio/task_predict_modality.git \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \
   --workspace 53907369739130 \
-  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --compute-env 5DwwhQoBi0knMSGcwThnlF \
   --params-file /tmp/params.yaml \
   --config common/nextflow_helpers/labels_tw.config \
   --labels task_predict_modality,test

scripts/run_benchmark/run_test_seqeracloud.sh

@@ -13,5 +13,5 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, lowmem, lowcpu]
+      label: [midtime, midmem, lowcpu]
 

src/control_methods/mean_per_gene/config.vsh.yaml

@@ -13,4 +13,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, lowmem, lowcpu]
+      label: [midtime, midmem, lowcpu]

src/control_methods/random_predict/config.vsh.yaml

@@ -13,4 +13,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, lowmem, lowcpu]
+      label: [midtime, midmem, lowcpu]

src/control_methods/solution/config.vsh.yaml

@@ -13,4 +13,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [midtime, lowmem, lowcpu]
+      label: [midtime, midmem, lowcpu]

src/control_methods/zeros/config.vsh.yaml

@@ -32,4 +32,4 @@ runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [hightime, lowmem, lowcpu]
+      label: [hightime, midmem, midcpu]