deploy: 00e7cf1

Author: rcannood

.github/workflows/integration-test.yml

@@ -121,6 +121,13 @@ jobs:
     - name: Run integration test
       timeout-minutes: 120
       run: |
+        # check if stub runs work
+        export NXF_VER=22.04.5
+        nextflow run . \
+          -main-script "target/nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
+          -stub -profile no_publish \
+          -c src/workflows/utils/integration_tests.config 
+
         # todo: replace with viash test command
         export NXF_VER=22.04.5
         nextflow run . \

.github/workflows/release-build.yml

@@ -109,6 +109,13 @@ jobs:
     - name: Run integration test
       timeout-minutes: 120
       run: |
+        # check if stub runs work
+        export NXF_VER=22.04.5
+        nextflow run . \
+          -main-script "target/nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
+          -stub -profile no_publish \
+          -c src/workflows/utils/integration_tests.config
+
         # todo: replace with viash test command
         export NXF_VER=22.04.5
         nextflow run . \

CHANGELOG.md

@@ -64,6 +64,8 @@
 
 # BUG FIXES
 
+* Fix `-stub` runs (PR #1000).
+
 * `cluster/leiden`: Fix an issue where insufficient shared memory (size of `/dev/shm`) causes the processing to hang.  
 
 * `utils/subset_vars`: Convert .var column used for subsetting of dtype "boolean" to dtype "bool" when it doesn't contain NaN values (PR #959).

src/workflows/annotation/harmony_knn/config.vsh.yaml

@@ -175,7 +175,7 @@ dependencies:
   - name: workflows/integration/harmony_leiden
     alias: harmony_leiden_workflow
   - name: labels_transfer/knn
-  - name: dataflow/split_h5mu
+  - name: workflows/multiomics/split_h5mu
   - name: dataflow/concatenate_h5mu
   - name: dimred/pca
   - name: feature_annotation/align_query_reference

src/workflows/annotation/harmony_knn/main.nf

@@ -179,6 +179,14 @@ workflow run_wf {
         // map the integrated query and reference datasets back to the state
         | map {id, state ->
             def outputDir = state.output
+            if (workflow.stubRun) {
+                def output_files = outputDir.listFiles()
+                def new_state = state + [
+                    "input": output_files[0],
+                    "reference": output_files[1],
+                ]
+                return [id, new_state]
+            }
             def files = readCsv(state.output_files.toUriString())
             def query_file = files.findAll{ dat -> dat.name == 'query' }
             assert query_file.size() == 1, 'there should only be one query file'

src/workflows/annotation/scanvi_scarches/config.vsh.yaml

@@ -7,6 +7,12 @@ authors:
   - __merge__: /src/authors/weiwei_schultz.yaml
     roles: [ contributor ]
 
+info:
+  name: "scANVI - scArches workflow"
+  test_dependencies:
+    - name: scanvi_scarches_test
+      namespace: test_workflows/annotation
+
 argument_groups:
   - name: Query Input
     arguments:

src/workflows/annotation/scanvi_scarches/main.nf

@@ -113,7 +113,7 @@ workflow run_wf {
               "obsp_neighbor_connectivities": "scanvi_integration_connectivities",
               "obs_cluster": "scanvi_integration_leiden",
               "obsm_umap": "X_scanvi_umap"
-          ]
+          ],
           toState: [ "output": "output" ]
         )
         | setState(["output", "output_model"])

src/workflows/annotation/scanvi_scarches/test.nf

@@ -52,6 +52,8 @@ workflow test_wf {
           "input": "output"
         ]
     )
+
+  output_ch
     | toSortedList({a, b -> a[0] <=> b[0]})
     | map { output_list ->
       assert output_list.size() == 1 : "output channel should contain 1 event"

src/workflows/annotation/scvi_knn/config.vsh.yaml

@@ -203,7 +203,7 @@ dependencies:
   - name: workflows/integration/scvi_leiden
     alias: scvi_leiden_workflow
   - name: labels_transfer/knn
-  - name: dataflow/split_h5mu
+  - name: workflows/multiomics/split_h5mu
   - name: dataflow/concatenate_h5mu
   - name: feature_annotation/align_query_reference
   - name: feature_annotation/highly_variable_features_scanpy

src/workflows/annotation/scvi_knn/main.nf

@@ -182,6 +182,14 @@ workflow run_wf {
       // map the integrated query and reference datasets back to the state
       | map {id, state ->
           def outputDir = state.output
+          if (workflow.stubRun) {
+            def output_files = outputDir.listFiles()
+            def new_state = state + [
+                "input": output_files[0],
+                "reference": output_files[1],
+            ]
+            return [id, new_state]
+          }
           def files = readCsv(state.output_files.toUriString())
           def query_file = files.findAll{ dat -> dat.name == 'query' }
           assert query_file.size() == 1, 'there should only be one query file'