diff --git a/src/methods/celloracle/config.vsh.yaml b/src/methods/celloracle/config.vsh.yaml index 07a9f0d9d..95faac1a7 100644 --- 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 index 88bee0726..607a61f0c 100644 --- 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 index 2f3a7d924..129666767 100644 --- 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/src/workflows/process_multiomics/config.novsh.yaml b/src/workflows/process_multiomics/config.vsh.yaml similarity index 100% rename from src/workflows/process_multiomics/config.novsh.yaml rename to src/workflows/process_multiomics/config.vsh.yaml