Merge pull request #5 from openproblems-bio/fix-components

lazappi · web-flow · commit 106edbdeae97 · 2025-09-10T08:23:26.000+02:00
diff --git a/scripts/create_test_resources/cxg_immune_cell_atlas.sh b/scripts/create_test_resources/cxg_immune_cell_atlas.sh
@@ -40,7 +40,7 @@ HERE
 
 nextflow run . \
   -main-script target/nextflow/workflows/scrnaseq/process_cellxgene_census/main.nf \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -profile docker \
   -params-file "/tmp/params.yaml"
 
diff --git a/scripts/create_test_resources/cxg_mouse_pancreas_atlas.sh b/scripts/create_test_resources/cxg_mouse_pancreas_atlas.sh
@@ -41,7 +41,7 @@ HERE
 
 nextflow run . \
   -main-script target/nextflow/workflows/scrnaseq/process_cellxgene_census/main.nf \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -profile docker \
   -params-file "/tmp/params.yaml"
 
diff --git a/scripts/create_test_resources/mouse_brain_coronal.sh b/scripts/create_test_resources/mouse_brain_coronal.sh
@@ -31,7 +31,7 @@ HERE
 
 nextflow run . \
   -main-script target/nextflow/workflows/spatial/process_tenx_visium/main.nf \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -profile docker \
   -params-file "/tmp/params.yaml"
 
diff --git a/scripts/create_test_resources/pancreas.sh b/scripts/create_test_resources/pancreas.sh
@@ -20,7 +20,7 @@ KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s
 nextflow run . \
   -main-script target/nextflow/workflows/scrnaseq/process_openproblems_v1/main.nf \
   -profile docker \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -resume \
   --id pancreas \
   --input_id pancreas \
diff --git a/src/workflows/extract_dataset_info/main.nf b/src/workflows/extract_dataset_info/main.nf
@@ -13,7 +13,7 @@ workflow run_wf {
   output_ch = input_ch
 
     // extract the dataset metadata
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: [input: "input"],
       toState: { id, output, state ->
         state + [
diff --git a/src/workflows/extract_dataset_info/run_test.sh b/src/workflows/extract_dataset_info/run_test.sh
@@ -23,7 +23,7 @@ nextflow run . \
   -main-script target/nextflow/workflows/extract_dataset_info/main.nf \
   -profile docker \
   -resume \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   -entry auto \
   --input_states "$DATASETS_DIR/**/state.yaml" \
   --rename_keys 'input:output_dataset' \
diff --git a/src/workflows/extract_dataset_meta/main.nf b/src/workflows/extract_dataset_meta/main.nf
@@ -6,7 +6,7 @@ workflow run_wf {
   output_ch = input_ch
 
     // extract the dataset metadata
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: [input: "input"],
       toState: [output: "output"]
     )
diff --git a/src/workflows/extract_dataset_meta/run_test.sh b/src/workflows/extract_dataset_meta/run_test.sh
@@ -23,7 +23,7 @@ nextflow run . \
   -main-script target/nextflow/workflows/extract_dataset_meta/main.nf \
   -profile docker \
   -resume \
-  -c src/wf_utils/labels_ci.config \
+  -c common/nextflow_helpers/labels_ci.config \
   --input $DATASETS_DIR \
   --output meta.yaml \
   --publish_dir "$OUTPUT_DIR"
diff --git a/src/workflows/multimodal/process_openproblems_neurips2021_bmmc/main.nf b/src/workflows/multimodal/process_openproblems_neurips2021_bmmc/main.nf
@@ -150,7 +150,7 @@ workflow run_wf {
       [id, state + ["output_mod1": state.hvg_mod1, "output_mod2": state.hvg_mod2]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod1",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod1")
@@ -166,7 +166,7 @@ workflow run_wf {
       toState: ["output_meta_mod1": "output"]
     )
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod2",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod2")
diff --git a/src/workflows/multimodal/process_openproblems_neurips2022_pbmc/main.nf b/src/workflows/multimodal/process_openproblems_neurips2022_pbmc/main.nf
@@ -146,7 +146,7 @@ workflow run_wf {
       [id, state + ["output_mod1": state.hvg_mod1, "output_mod2": state.hvg_mod2]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod1",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod1")
@@ -162,7 +162,7 @@ workflow run_wf {
       toState: ["output_meta_mod1": "output"]
     )
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod2",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod2")
diff --git a/src/workflows/multimodal/process_openproblems_v1_multimodal/main.nf b/src/workflows/multimodal/process_openproblems_v1_multimodal/main.nf
@@ -158,7 +158,7 @@ workflow run_wf {
       ]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod1",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod1")
@@ -174,7 +174,7 @@ workflow run_wf {
       toState: ["output_meta_mod1": "output"]
     )
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       key: "extract_metadata_mod2",
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_mod2")
diff --git a/src/workflows/scrnaseq/process_cellxgene_census/main.nf b/src/workflows/scrnaseq/process_cellxgene_census/main.nf
@@ -128,7 +128,7 @@ workflow run_wf {
       [id, state + [output_dataset: state.output_knn]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_dataset")
         // workaround: convert GString to String
diff --git a/src/workflows/scrnaseq/process_openproblems_v1/main.nf b/src/workflows/scrnaseq/process_openproblems_v1/main.nf
@@ -126,7 +126,7 @@ workflow run_wf {
       [id, state + [output_dataset: state.output_knn]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_dataset")
         // workaround: convert GString to String
diff --git a/src/workflows/spatial/process_tenx_visium/main.nf b/src/workflows/spatial/process_tenx_visium/main.nf
@@ -106,7 +106,7 @@ workflow run_wf {
       [id, state + [output_dataset: state.output_normalized]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_dataset")
         // workaround: convert GString to String
diff --git a/src/workflows/spatial/process_zenodo/main.nf b/src/workflows/spatial/process_zenodo/main.nf
@@ -105,7 +105,7 @@ workflow run_wf {
       [id, state + [output_dataset: state.output_normalized]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_dataset")
         // workaround: convert GString to String
diff --git a/src/workflows/spatial/process_zenodo_slidetags/main.nf b/src/workflows/spatial/process_zenodo_slidetags/main.nf
@@ -105,7 +105,7 @@ workflow run_wf {
       [id, state + [output_dataset: state.output_normalized]]
     }
 
-    | extract_metadata.run(
+    | extract_uns_metadata.run(
       fromState: { id, state ->
         def schema = findArgumentSchema(meta.config, "output_dataset")
         // workaround: convert GString to String

Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@ workflow run_wf {`
`6`	`6`	`output_ch = input_ch`
`7`	`7`
`8`	`8`	`// extract the dataset metadata`
`9`		`- \| extract_metadata.run(`
	`9`	`+ \| extract_uns_metadata.run(`
`10`	`10`	`fromState: [input: "input"],`
`11`	`11`	`toState: [output: "output"]`
`12`	`12`	`)`