fix references to renamed components

openproblems-bio · Oct 25, 2024 · 73f3c22 · 73f3c22
1 parent 1af28fb
commit 73f3c22
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Showing 9 changed files with 9 additions and 14 deletions.
diff --git a/src/datasets/workflows/scrnaseq/process_cellxgene_census/config.vsh.yaml b/src/datasets/workflows/scrnaseq/process_cellxgene_census/config.vsh.yaml
@@ -200,7 +200,7 @@ dependencies:
   - name: datasets/processors/pca
   - name: datasets/processors/hvg
   - name: datasets/processors/knn
-  - name: common/extract_metadata
+  - name: utils/extract_uns_metadata
   # test_resources:
   #   - type: nextflow_script
   #     path: main.nf

diff --git a/src/datasets/workflows/scrnaseq/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/scrnaseq/process_openproblems_v1/config.vsh.yaml
@@ -158,7 +158,7 @@ dependencies:
   - name: datasets/processors/pca
   - name: datasets/processors/hvg
   - name: datasets/processors/knn
-  - name: common/extract_metadata
+  - name: utils/extract_uns_metadata
   # test_resources:
   #   - type: nextflow_script
   #     path: main.nf

diff --git a/src/datasets/workflows/spatial/process_tenx_visium/config.vsh.yaml b/src/datasets/workflows/spatial/process_tenx_visium/config.vsh.yaml
@@ -138,6 +138,6 @@ dependencies:
   - name: datasets/normalization/sqrt_cp
   - name: datasets/normalization/l1_sqrt
   - name: datasets/processors/subsample
-  - name: common/extract_metadata
+  - name: utils/extract_uns_metadata
 runners:
   - type: nextflow
diff --git a/src/datasets/workflows/spatial/process_zenodo/config.vsh.yaml b/src/datasets/workflows/spatial/process_zenodo/config.vsh.yaml
@@ -134,6 +134,6 @@ dependencies:
   - name: datasets/normalization/sqrt_cp
   - name: datasets/normalization/l1_sqrt
   - name: datasets/processors/subsample
-  - name: common/extract_metadata
+  - name: utils/extract_uns_metadata
 runners:
   - type: nextflow
diff --git a/src/datasets/workflows/spatial/process_zenodo_slidetags/config.vsh.yaml b/src/datasets/workflows/spatial/process_zenodo_slidetags/config.vsh.yaml
@@ -134,6 +134,6 @@ dependencies:
   - name: datasets/normalization/sqrt_cp
   - name: datasets/normalization/l1_sqrt
   - name: datasets/processors/subsample
-  - name: common/extract_metadata
+  - name: utils/extract_uns_metadata
 runners:
   - type: nextflow
diff --git a/src/reporting/process_dataset_metadata/run.sh b/src/reporting/process_dataset_metadata/run.sh
@@ -37,7 +37,7 @@ for LOADER in $(aws s3 ls $DATASET_DIR); do
 
       # start the 
       NXF_VER=23.10.0 nextflow run . \
-      -main-script target/nextflow/common/process_dataset_metadata/run/main.nf \
+      -main-script target/nextflow/reporting/process_dataset_metadata/main.nf \
       -profile docker \
       -c src/wf_utils/labels_ci.config \
       --id "extract_metadata" \

diff --git a/src/reporting/process_task_results/main.nf b/src/reporting/process_task_results/main.nf
@@ -5,9 +5,8 @@ workflow run_wf {
   main:
   output_ch = input_ch
 
-    | get_task_info.run(
-      key: "task_info",
       fromState: [ 
+    | get_task_info.run(
         "input": "input_task_info"
       ],
       toState: ["output_task": "output"]
@@ -22,30 +21,26 @@ workflow run_wf {
     | get_method_info.run(
       fromState: [ 
         "input": "input_method_configs",
-        "task_id" : "task_id"
       ],
       toState: ["output_method": "output"]
     )
 
     | get_metric_info.run(
       fromState: [ 
         "input": "input_metric_configs",
-        "task_id" : "task_id"
       ],
       toState: ["output_metric": "output"]
     )
 
     | get_dataset_info.run(
       fromState: [
-        "task_id" : "task_id",
         "input": "input_dataset_info",
       ],
       toState: ["output_dataset": "output"]
     )
 
     | get_results.run(
       fromState: [ 
-        "task_id": "task_id",
         "input_scores": "input_scores",
         "input_execution": "input_execution",
         "input_dataset_info": "output_dataset",

diff --git a/src/reporting/process_task_results/run_nf_tower_test.sh b/src/reporting/process_task_results/run_nf_tower_test.sh
@@ -31,7 +31,7 @@ HERE
 tw launch https://github.com/openproblems-bio/openproblems.git \
   --revision main_build \
   --pull-latest \
-  --main-script target/nextflow/common/workflows/transform_meta/main.nf \
+  --main-script target/nextflow/reporting/process_task_results/main.nf \
   --workspace 53907369739130 \
   --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
   --params-file /tmp/params.yaml \

diff --git a/src/reporting/process_task_results/run_test.sh b/src/reporting/process_task_results/run_test.sh
@@ -24,7 +24,7 @@ for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_pr
 
   # start the run
   NXF_VER=23.10.0 nextflow run . \
-    -main-script target/nextflow/common/process_task_results/run/main.nf \
+    -main-script target/nextflow/reporting/process_task_results/main.nf \
     -profile docker \
     -resume \
     -c src/wf_utils/labels_ci.config \