test issues fixed

openproblems-bio · Aug 1, 2024 · bf8ba9f · bf8ba9f
1 parent 9928733
commit bf8ba9f
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/src/methods/celloracle/config.vsh.yaml b/src/methods/celloracle/config.vsh.yaml
@@ -11,16 +11,19 @@ functionality:
   arguments:
     - name: --multiomics_rna
       __merge__: ../../api/file_multiomics_rna_h5ad.yaml
-      required: True
+      required: false
       direction: input
+      default: resources_test/grn-benchmark/multiomics_rna.h5ad
     - name: --multiomics_atac
       __merge__: ../../api/file_multiomics_atac_h5ad.yaml
       required: false
       direction: input
+      default: resources_test/grn-benchmark/multiomics_atac.h5ad
     - name: --prediction
       __merge__: ../../api/file_prediction.yaml
-      required: true
+      required: false
       direction: output
+      default: resources_test/grn-benchmark/perturbation_data.h5ad
 
     - name: --temp_dir
       type: string
@@ -39,12 +42,13 @@ functionality:
 
 platforms:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_python:1.0.4
-    setup:
-      - type: python
-        packages: [celloracle==0.14.0, genomepy==0.16.1]
-      - type: apt
-        packages: []
+    # image: ghcr.io/openproblems-bio/base_python:1.0.4
+    image: kenjikamimoto126/celloracle_ubuntu:0.18.0
+    # setup:
+    #   - type: python
+    #     packages: [celloracle==0.14.0, genomepy==0.16.1]
+    #   - type: apt
+    #     packages: []
 
   - type: native
   - type: nextflow

diff --git a/src/methods/dummy/config.vsh.yaml b/src/methods/dummy/config.vsh.yaml
@@ -1,4 +1,3 @@
-__merge__: ../../api/comp_method.yaml
 
 functionality:
   name: dummy

diff --git a/src/process_data/multiomics/format_data/config.vsh.yaml b/src/process_data/multiomics/format_data/config.vsh.yaml
@@ -1,4 +1,3 @@
-__merge__: ../../../api/comp_method.yaml
 
 functionality:
   name: multiome

diff --git a/...lows/process_multiomics/config.novsh.yaml → ...kflows/process_multiomics/config.vsh.yaml b/...lows/process_multiomics/config.novsh.yaml → ...kflows/process_multiomics/config.vsh.yaml