move files

openproblems-bio · rcannood · Jun 4, 2024 · Jun 4, 2024 · Jun 4, 2024 · Jun 4, 2024
commit aee68bf0cdea5315f79f97339567889360e2a7c9
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,9 +2,9 @@
 
 Initial release of the Perturbation Prediction task. Initial components:
 
-* `src/task/process_dataset`: Compute the DGE data from the raw single-cell counts using Limma.
-* `src/task/control_methods`: Baseline control methods: sample, ground_truth, zeros, mean_across_celltypes, mean_across_compounds, mean_outcome.
-* `src/task/methods`: Perturbation prediction methods: jn_ap_op2, lgc_ensemble, nn_retraining_with_pseudolabels, pyboost, scape, transformer_ensemble.
-* `src/task/metrics`: Evaluation metrics: mean_rowwise_error, mean_rowwise_correlation.
+* `src/process_dataset`: Compute the DGE data from the raw single-cell counts using Limma.
+* `src/control_methods`: Baseline control methods: sample, ground_truth, zeros, mean_across_celltypes, mean_across_compounds, mean_outcome.
+* `src/methods`: Perturbation prediction methods: jn_ap_op2, lgc_ensemble, nn_retraining_with_pseudolabels, pyboost, scape, transformer_ensemble.
+* `src/metrics`: Evaluation metrics: mean_rowwise_error, mean_rowwise_correlation.
 
 
diff --git a/scripts/add_a_method.sh b/scripts/add_a_method.sh
@@ -15,25 +15,25 @@ viash run src/common/create_component/config.vsh.yaml -- \
   --language "$method_lang" \
   --name "$method_id"
 
-# TODO: fill in required fields in src/task/methods/foo/config.vsh.yaml
-# TODO: edit src/task/methods/foo/script.py/R
+# TODO: fill in required fields in src/methods/foo/config.vsh.yaml
+# TODO: edit src/methods/foo/script.py/R
 
 # test the component
-viash test src/task/methods/$method_id/config.vsh.yaml
+viash test src/methods/$method_id/config.vsh.yaml
 
 # rebuild the container (only if you change something to the docker platform)
 # You can reduce the memory and cpu allotted to jobs in _viash.yaml by modifying .platforms[.type == "nextflow"].config.labels
-viash run src/task/methods/$method_id/config.vsh.yaml -- \
+viash run src/methods/$method_id/config.vsh.yaml -- \
   ---setup cachedbuild ---verbose
 
 # run the method (using h5ad as input)
-viash run src/task/methods/$method_id/config.vsh.yaml -- \
+viash run src/methods/$method_id/config.vsh.yaml -- \
   --de_train_h5ad "resources/neurips-2023-kaggle/2023-09-12_de_by_cell_type_train.h5ad" \
   --id_map "resources/neurips-2023-kaggle/id_map.csv" \
   --output "output/prediction.h5ad"
 
 # run evaluation metric
-viash run src/task/metrics/mean_rowwise_error/config.vsh.yaml -- \
+viash run src/metrics/mean_rowwise_error/config.vsh.yaml -- \
   --de_test_h5ad "resources/neurips-2023-kaggle/de_test.h5ad" \
   --prediction "output/prediction.h5ad" \
   --output "output/score.h5ad"

diff --git a/scripts/generate_kaggle_resources.sh b/scripts/generate_kaggle_resources.sh
@@ -18,7 +18,7 @@ if [[ ! -f "$OUT/2023-09-12_de_by_cell_type_test.h5ad" ]]; then
     "import anndata as ad; ad.read_h5ad('$OUT/2023-09-12_de_by_cell_type_train.h5ad').write_h5ad('$OUT/2023-09-12_de_by_cell_type_train.h5ad', compression='gzip')"
 fi
 
-viash run src/task/process_dataset/convert_kaggle_h5ad_to_parquet/config.vsh.yaml -- \
+viash run src/process_dataset/convert_kaggle_h5ad_to_parquet/config.vsh.yaml -- \
   --input_train "$OUT/2023-09-12_de_by_cell_type_train.h5ad" \
   --input_test "$OUT/2023-09-12_de_by_cell_type_test.h5ad" \
   --input_single_cell_h5ad "resources/neurips-2023-raw/sc_counts.h5ad" \
@@ -34,14 +34,14 @@ viash run src/task/process_dataset/convert_kaggle_h5ad_to_parquet/config.vsh.yam
   --dataset_organism homo_sapiens
 
 echo ">> Run method"
-viash run src/task/control_methods/mean_across_compounds/config.vsh.yaml -- \
+viash run src/control_methods/mean_across_compounds/config.vsh.yaml -- \
   --de_train_h5ad "$OUT/de_train.h5ad" \
   --de_test_h5ad "$OUT/de_test.h5ad" \
   --id_map "$OUT/id_map.csv" \
   --output "$OUT/prediction.h5ad"
 
 echo ">> Run metric"
-viash run src/task/metrics/mean_rowwise_error/config.vsh.yaml -- \
+viash run src/metrics/mean_rowwise_error/config.vsh.yaml -- \
   --prediction "$OUT/prediction.h5ad" \
   --de_test_h5ad "$OUT/de_test.h5ad" \
   --output "$OUT/score.h5ad"

diff --git a/scripts/generate_resources.sh b/scripts/generate_resources.sh
@@ -32,14 +32,14 @@ nextflow run \
   --publish_dir "$OUT"
 
 echo ">> Run method"
-viash run src/task/control_methods/mean_across_compounds/config.vsh.yaml -- \
+viash run src/control_methods/mean_across_compounds/config.vsh.yaml -- \
   --de_train_h5ad "$OUT/de_train.h5ad" \
   --de_test_h5ad "$OUT/de_test.h5ad" \
   --id_map "$OUT/id_map.csv" \
   --output "$OUT/prediction.h5ad"
 
 echo ">> Run metric"
-viash run src/task/metrics/mean_rowwise_error/config.vsh.yaml -- \
+viash run src/metrics/mean_rowwise_error/config.vsh.yaml -- \
   --prediction "$OUT/prediction.h5ad" \
   --de_test_h5ad "$OUT/de_test.h5ad" \
   --output "$OUT/score.h5ad"

diff --git a/scripts/render_readme.sh b/scripts/render_readme.sh
@@ -5,7 +5,7 @@ set -e
 [[ ! -d ../openproblems-v2 ]] && echo "You need to clone the openproblems-v2 repository next to this repository" && exit 1
 
 ../openproblems-v2/target/docker/common/create_task_readme/create_task_readme \
-  --task "dge_perturbation_prediction" \
-  --task_dir "src/task" \
+  --task "perturbation_prediction" \
+  --task_dir "src" \
   --github_url "https://github.com/openproblems-bio/task_perturbation_prediction/tree/main/" \
   --output "README.md"
diff --git a/scripts/run_benchmark_tw.sh b/scripts/run_benchmark_tw.sh
@@ -2,7 +2,7 @@
 
 RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)"
 resources_dir="s3://openproblems-bio/public/neurips-2023-competition/workflow-resources"
-publish_dir="s3://openproblems-data/resources/dge_perturbation_prediction/results/${RUN_ID}"
+publish_dir="s3://openproblems-data/resources/perturbation_prediction/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
 param_list:

diff --git a/scripts/run_benchmark_tw_traens.sh b/scripts/run_benchmark_tw_traens.sh
@@ -4,7 +4,7 @@
 
 RUN_ID="traens_$(date +%Y-%m-%d_%H-%M-%S)"
 resources_dir="s3://openproblems-bio/public/neurips-2023-competition/workflow-resources"
-publish_dir="s3://openproblems-data/resources/dge_perturbation_prediction/results/${RUN_ID}"
+publish_dir="s3://openproblems-data/resources/perturbation_prediction/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
 param_list:

diff --git a/scripts/run_layert_tw.sh b/scripts/run_layert_tw.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 RUN_ID="layert_$(date +%Y-%m-%d_%H-%M-%S)"
-publish_dir="s3://openproblems-data/resources/dge_perturbation_prediction/results/${RUN_ID}"
+publish_dir="s3://openproblems-data/resources/perturbation_prediction/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
 id: dge_perturbation_task

diff --git a/scripts/run_stability_tw.sh b/scripts/run_stability_tw.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 RUN_ID="stability_$(date +%Y-%m-%d_%H-%M-%S)"
-publish_dir="s3://openproblems-data/resources/dge_perturbation_prediction/results/${RUN_ID}"
+publish_dir="s3://openproblems-data/resources/perturbation_prediction/results/${RUN_ID}"
 
 cat > /tmp/params.yaml << HERE
 id: neurips-2023-data

diff --git a/scripts/sync_results.sh b/scripts/sync_results.sh
@@ -1,18 +1,18 @@
 #!/bin/bash
 
 aws s3 sync \
-  s3://openproblems-data/resources/dge_perturbation_prediction/results/ \
+  s3://openproblems-data/resources/perturbation_prediction/results/ \
   output/benchmark_results/ \
   --delete --dryrun
 
 # sync back modified results
 aws s3 sync \
   output/benchmark_results/ \
-  s3://openproblems-data/resources/dge_perturbation_prediction/results/ \
+  s3://openproblems-data/resources/perturbation_prediction/results/ \
   --delete --dryrun
 
 # sync one run
 runid=run_2024-06-01_00-03-09; aws s3 sync \
   output/benchmark_results/${runid}/ \
-  s3://openproblems-data/resources/dge_perturbation_prediction/results/${runid}/ \
+  s3://openproblems-data/resources/perturbation_prediction/results/${runid}/ \
   --delete --dryrun
diff --git a/src/task/api/comp_control_method.yaml → src/api/comp_control_method.yaml b/src/task/api/comp_control_method.yaml → src/api/comp_control_method.yaml
diff --git a/src/task/api/comp_method.yaml → src/api/comp_method.yaml b/src/task/api/comp_method.yaml → src/api/comp_method.yaml
diff --git a/src/task/api/comp_method_notest.yaml → src/api/comp_method_notest.yaml b/src/task/api/comp_method_notest.yaml → src/api/comp_method_notest.yaml
diff --git a/src/task/api/comp_metric.yaml → src/api/comp_metric.yaml b/src/task/api/comp_metric.yaml → src/api/comp_metric.yaml
diff --git a/src/task/api/comp_process_dataset.yaml → src/api/comp_process_dataset.yaml b/src/task/api/comp_process_dataset.yaml → src/api/comp_process_dataset.yaml
diff --git a/src/task/api/file_de_test_h5ad.yaml → src/api/file_de_test_h5ad.yaml b/src/task/api/file_de_test_h5ad.yaml → src/api/file_de_test_h5ad.yaml
diff --git a/src/task/api/file_de_train_h5ad.yaml → src/api/file_de_train_h5ad.yaml b/src/task/api/file_de_train_h5ad.yaml → src/api/file_de_train_h5ad.yaml
diff --git a/src/task/api/file_id_map.yaml → src/api/file_id_map.yaml b/src/task/api/file_id_map.yaml → src/api/file_id_map.yaml
diff --git a/src/task/api/file_prediction.yaml → src/api/file_prediction.yaml b/src/task/api/file_prediction.yaml → src/api/file_prediction.yaml
diff --git a/src/task/api/file_sc_counts.yaml → src/api/file_sc_counts.yaml b/src/task/api/file_sc_counts.yaml → src/api/file_sc_counts.yaml
diff --git a/src/task/api/file_score.yaml → src/api/file_score.yaml b/src/task/api/file_score.yaml → src/api/file_score.yaml
diff --git a/src/task/api/task_info.yaml → src/api/task_info.yaml b/src/task/api/task_info.yaml → src/api/task_info.yaml
diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml
@@ -24,7 +24,7 @@ functionality:
       direction: output
       # required: true
       description: Path to the component directory. Suggested location is `src/<TASK>/<TYPE>s/<NAME>`.
-      default: src/task/methods/${VIASH_PAR_NAME}
+      default: src/methods/${VIASH_PAR_NAME}
     - type: file
       name: --api_file
       description: |
@@ -33,7 +33,7 @@ functionality:
         to manually specify a different API file to inherit from.
       must_exist: false
       # required: true
-      default: src/task/api/comp_method.yaml
+      default: src/api/comp_method.yaml
     - type: file
       name: --viash_yaml
       description: |

diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py
@@ -10,8 +10,8 @@
   "type": "method",
   "language": "python",
   "name": "new_comp",
-  "output": "src/task/method/new_comp",
-  "api_file": "src/task/api/comp_method.yaml",
+  "output": "src/method/new_comp",
+  "api_file": "src/api/comp_method.yaml",
   "viash_yaml": "_viash.yaml"
 }
 ## VIASH END

diff --git a/...trol_methods/ground_truth/config.vsh.yaml → ...trol_methods/ground_truth/config.vsh.yaml b/...trol_methods/ground_truth/config.vsh.yaml → ...trol_methods/ground_truth/config.vsh.yaml
diff --git a/...ask/control_methods/ground_truth/script.R → src/control_methods/ground_truth/script.R b/...ask/control_methods/ground_truth/script.R → src/control_methods/ground_truth/script.R
diff --git a/...ods/mean_across_celltypes/config.vsh.yaml → ...ods/mean_across_celltypes/config.vsh.yaml b/...ods/mean_across_celltypes/config.vsh.yaml → ...ods/mean_across_celltypes/config.vsh.yaml
diff --git a/...l_methods/mean_across_celltypes/script.py → ...l_methods/mean_across_celltypes/script.py b/...l_methods/mean_across_celltypes/script.py → ...l_methods/mean_across_celltypes/script.py
diff --git a/...ods/mean_across_compounds/config.vsh.yaml → ...ods/mean_across_compounds/config.vsh.yaml b/...ods/mean_across_compounds/config.vsh.yaml → ...ods/mean_across_compounds/config.vsh.yaml
diff --git a/...l_methods/mean_across_compounds/script.py → ...l_methods/mean_across_compounds/script.py b/...l_methods/mean_across_compounds/script.py → ...l_methods/mean_across_compounds/script.py
diff --git a/...trol_methods/mean_outcome/config.vsh.yaml → ...trol_methods/mean_outcome/config.vsh.yaml b/...trol_methods/mean_outcome/config.vsh.yaml → ...trol_methods/mean_outcome/config.vsh.yaml
diff --git a/...sk/control_methods/mean_outcome/script.py → src/control_methods/mean_outcome/script.py b/...sk/control_methods/mean_outcome/script.py → src/control_methods/mean_outcome/script.py
diff --git a/...sk/control_methods/sample/config.vsh.yaml → src/control_methods/sample/config.vsh.yaml b/...sk/control_methods/sample/config.vsh.yaml → src/control_methods/sample/config.vsh.yaml
diff --git a/src/task/control_methods/sample/script.R → src/control_methods/sample/script.R b/src/task/control_methods/sample/script.R → src/control_methods/sample/script.R
diff --git a/...ask/control_methods/zeros/config.vsh.yaml → src/control_methods/zeros/config.vsh.yaml b/...ask/control_methods/zeros/config.vsh.yaml → src/control_methods/zeros/config.vsh.yaml
diff --git a/src/task/control_methods/zeros/script.py → src/control_methods/zeros/script.py b/src/task/control_methods/zeros/script.py → src/control_methods/zeros/script.py
diff --git a/src/task/methods/jn_ap_op2/config.vsh.yaml → src/methods/jn_ap_op2/config.vsh.yaml b/src/task/methods/jn_ap_op2/config.vsh.yaml → src/methods/jn_ap_op2/config.vsh.yaml
diff --git a/src/task/methods/jn_ap_op2/helper.py → src/methods/jn_ap_op2/helper.py b/src/task/methods/jn_ap_op2/helper.py → src/methods/jn_ap_op2/helper.py
diff --git a/src/task/methods/jn_ap_op2/script.py → src/methods/jn_ap_op2/script.py b/src/task/methods/jn_ap_op2/script.py → src/methods/jn_ap_op2/script.py
@@ -20,7 +20,7 @@
     "submission_names": ["dl40"]
 }
 meta = {
-    "resources_dir": "src/task/methods/jn_ap_op2",
+    "resources_dir": "src/methods/jn_ap_op2",
 }
 ## VIASH END
 

diff --git a/...task/methods/lgc_ensemble/config.vsh.yaml → src/methods/lgc_ensemble/config.vsh.yaml b/...task/methods/lgc_ensemble/config.vsh.yaml → src/methods/lgc_ensemble/config.vsh.yaml
diff --git a/src/task/methods/lgc_ensemble/main.nf → src/methods/lgc_ensemble/main.nf b/src/task/methods/lgc_ensemble/main.nf → src/methods/lgc_ensemble/main.nf
diff --git a/src/task/methods/lgc_ensemble/test.sh → src/methods/lgc_ensemble/test.sh b/src/task/methods/lgc_ensemble/test.sh → src/methods/lgc_ensemble/test.sh
diff --git a/...thods/lgc_ensemble_direct/config.vsh.yaml → ...thods/lgc_ensemble_direct/config.vsh.yaml b/...thods/lgc_ensemble_direct/config.vsh.yaml → ...thods/lgc_ensemble_direct/config.vsh.yaml
diff --git a/...ask/methods/lgc_ensemble_direct/script.py → src/methods/lgc_ensemble_direct/script.py b/...ask/methods/lgc_ensemble_direct/script.py → src/methods/lgc_ensemble_direct/script.py
@@ -19,7 +19,7 @@
     "output_model": None
 }
 meta = {
-    "resources_dir": "src/task/methods/lgc_ensemble",
+    "resources_dir": "src/methods/lgc_ensemble",
     "temp_dir": "/tmp"
 }
 ## VIASH END

diff --git a/...ds/lgc_ensemble_helpers/divisor_finder.py → ...ds/lgc_ensemble_helpers/divisor_finder.py b/...ds/lgc_ensemble_helpers/divisor_finder.py → ...ds/lgc_ensemble_helpers/divisor_finder.py
diff --git a/...ds/lgc_ensemble_helpers/helper_classes.py → ...ds/lgc_ensemble_helpers/helper_classes.py b/...ds/lgc_ensemble_helpers/helper_classes.py → ...ds/lgc_ensemble_helpers/helper_classes.py
diff --git a/.../lgc_ensemble_helpers/helper_functions.py → .../lgc_ensemble_helpers/helper_functions.py b/.../lgc_ensemble_helpers/helper_functions.py → .../lgc_ensemble_helpers/helper_functions.py
diff --git a/...sk/methods/lgc_ensemble_helpers/models.py → src/methods/lgc_ensemble_helpers/models.py b/...sk/methods/lgc_ensemble_helpers/models.py → src/methods/lgc_ensemble_helpers/models.py
diff --git a/...k/methods/lgc_ensemble_helpers/predict.py → src/methods/lgc_ensemble_helpers/predict.py b/...k/methods/lgc_ensemble_helpers/predict.py → src/methods/lgc_ensemble_helpers/predict.py
diff --git a/...hods/lgc_ensemble_helpers/prepare_data.py → ...hods/lgc_ensemble_helpers/prepare_data.py b/...hods/lgc_ensemble_helpers/prepare_data.py → ...hods/lgc_ensemble_helpers/prepare_data.py
diff --git a/...ask/methods/lgc_ensemble_helpers/train.py → src/methods/lgc_ensemble_helpers/train.py b/...ask/methods/lgc_ensemble_helpers/train.py → src/methods/lgc_ensemble_helpers/train.py
diff --git a/...hods/lgc_ensemble_predict/config.vsh.yaml → ...hods/lgc_ensemble_predict/config.vsh.yaml b/...hods/lgc_ensemble_predict/config.vsh.yaml → ...hods/lgc_ensemble_predict/config.vsh.yaml
diff --git a/...sk/methods/lgc_ensemble_predict/script.py → src/methods/lgc_ensemble_predict/script.py b/...sk/methods/lgc_ensemble_predict/script.py → src/methods/lgc_ensemble_predict/script.py
diff --git a/...hods/lgc_ensemble_prepare/config.vsh.yaml → ...hods/lgc_ensemble_prepare/config.vsh.yaml b/...hods/lgc_ensemble_prepare/config.vsh.yaml → ...hods/lgc_ensemble_prepare/config.vsh.yaml
diff --git a/...sk/methods/lgc_ensemble_prepare/script.py → src/methods/lgc_ensemble_prepare/script.py b/...sk/methods/lgc_ensemble_prepare/script.py → src/methods/lgc_ensemble_prepare/script.py
@@ -22,7 +22,7 @@
     "train_data_aug_dir": "output/train_data_aug_dir",
 }
 meta = {
-    "resources_dir": "src/task/methods/lgc_ensemble",
+    "resources_dir": "src/methods/lgc_ensemble",
     "temp_dir": "/tmp"
 }
 ## VIASH END
@@ -37,7 +37,7 @@
 
 
 ###################################################################
-# interpreted from src/task/methods/lgc_ensemble/prepare_data.py
+# interpreted from src/methods/lgc_ensemble/prepare_data.py
 # prepare data
 seed_everything()
 
@@ -91,7 +91,7 @@
 _, _ = save_ChemBERTa_features(test_smiles, out_dir=par["train_data_aug_dir"], on_train_data=False)
 
 ###################################################################
-# interpreted from src/task/methods/lgc_ensemble/train.py
+# interpreted from src/methods/lgc_ensemble/train.py
 
 ## Prepare cross-validation
 cell_types_sm_names = de_train[['cell_type', 'sm_name']]

diff --git a/...ethods/lgc_ensemble_train/config.vsh.yaml → ...ethods/lgc_ensemble_train/config.vsh.yaml b/...ethods/lgc_ensemble_train/config.vsh.yaml → ...ethods/lgc_ensemble_train/config.vsh.yaml
diff --git a/...task/methods/lgc_ensemble_train/script.py → src/methods/lgc_ensemble_train/script.py b/...task/methods/lgc_ensemble_train/script.py → src/methods/lgc_ensemble_train/script.py
@@ -18,7 +18,7 @@
     "log_file": "output/log.json",
 }
 meta = {
-    "resources_dir": "src/task/methods/lgc_ensemble",
+    "resources_dir": "src/methods/lgc_ensemble",
     "temp_dir": "/tmp"
 }
 ## VIASH END
@@ -32,7 +32,7 @@
 from helper_functions import train_function
 
 ###################################################################
-# Interpretation from src/task/methods/lgc_ensemble/helper_functions.py
+# Interpretation from src/methods/lgc_ensemble/helper_functions.py
 
 print("Load data...", flush=True)
 # read kf_cv_initial from json

diff --git a/...raining_with_pseudolabels/config.vsh.yaml → ...raining_with_pseudolabels/config.vsh.yaml b/...raining_with_pseudolabels/config.vsh.yaml → ...raining_with_pseudolabels/config.vsh.yaml
diff --git a/...raining_with_pseudolabels/notebook_264.py → ...raining_with_pseudolabels/notebook_264.py b/...raining_with_pseudolabels/notebook_264.py → ...raining_with_pseudolabels/notebook_264.py
diff --git a/...raining_with_pseudolabels/notebook_266.py → ...raining_with_pseudolabels/notebook_266.py b/...raining_with_pseudolabels/notebook_266.py → ...raining_with_pseudolabels/notebook_266.py
diff --git a/...nn_retraining_with_pseudolabels/script.py → ...nn_retraining_with_pseudolabels/script.py b/...nn_retraining_with_pseudolabels/script.py → ...nn_retraining_with_pseudolabels/script.py
@@ -26,7 +26,7 @@
     "output": "output.h5ad",
     "reps": 2,
 }
-meta = {"resources_dir": "src/task/methods/nn_retraining_with_pseudolabels"}
+meta = {"resources_dir": "src/methods/nn_retraining_with_pseudolabels"}
 ## VIASH END
 
 # load helper functions in notebooks

diff --git a/src/task/methods/pyboost/config.vsh.yaml → src/methods/pyboost/config.vsh.yaml b/src/task/methods/pyboost/config.vsh.yaml → src/methods/pyboost/config.vsh.yaml
diff --git a/src/task/methods/pyboost/helper.py → src/methods/pyboost/helper.py b/src/task/methods/pyboost/helper.py → src/methods/pyboost/helper.py
diff --git a/src/task/methods/pyboost/script.py → src/methods/pyboost/script.py b/src/task/methods/pyboost/script.py → src/methods/pyboost/script.py
@@ -20,7 +20,7 @@
     output = "output.h5ad",
 )
 meta = dict(
-    resources_dir = "src/task/methods/pyboost"
+    resources_dir = "src/methods/pyboost"
 )
 ## VIASH END
 

diff --git a/src/task/methods/scape/config.vsh.yaml → src/methods/scape/config.vsh.yaml b/src/task/methods/scape/config.vsh.yaml → src/methods/scape/config.vsh.yaml
diff --git a/src/task/methods/scape/script.py → src/methods/scape/script.py b/src/task/methods/scape/script.py → src/methods/scape/script.py
diff --git a/...hods/transformer_ensemble/config.vsh.yaml → ...hods/transformer_ensemble/config.vsh.yaml b/...hods/transformer_ensemble/config.vsh.yaml → ...hods/transformer_ensemble/config.vsh.yaml
diff --git a/...sk/methods/transformer_ensemble/models.py → src/methods/transformer_ensemble/models.py b/...sk/methods/transformer_ensemble/models.py → src/methods/transformer_ensemble/models.py
diff --git a/...sk/methods/transformer_ensemble/script.py → src/methods/transformer_ensemble/script.py b/...sk/methods/transformer_ensemble/script.py → src/methods/transformer_ensemble/script.py
@@ -19,7 +19,7 @@
     "layer": "sign_log10_pval"
 }
 meta = {
-    "resources_dir": "src/task/methods/transformer_ensemble",
+    "resources_dir": "src/methods/transformer_ensemble",
 }
 ## VIASH END
 

diff --git a/...ask/methods/transformer_ensemble/train.py → src/methods/transformer_ensemble/train.py b/...ask/methods/transformer_ensemble/train.py → src/methods/transformer_ensemble/train.py
diff --git a/...ask/methods/transformer_ensemble/utils.py → src/methods/transformer_ensemble/utils.py b/...ask/methods/transformer_ensemble/utils.py → src/methods/transformer_ensemble/utils.py
diff --git a/.../mean_rowwise_correlation/config.vsh.yaml → .../mean_rowwise_correlation/config.vsh.yaml b/.../mean_rowwise_correlation/config.vsh.yaml → .../mean_rowwise_correlation/config.vsh.yaml
diff --git a/...metrics/mean_rowwise_correlation/script.R → ...metrics/mean_rowwise_correlation/script.R b/...metrics/mean_rowwise_correlation/script.R → ...metrics/mean_rowwise_correlation/script.R
diff --git a/...etrics/mean_rowwise_error/config.vsh.yaml → ...etrics/mean_rowwise_error/config.vsh.yaml b/...etrics/mean_rowwise_error/config.vsh.yaml → ...etrics/mean_rowwise_error/config.vsh.yaml
diff --git a/src/task/metrics/mean_rowwise_error/script.R → src/metrics/mean_rowwise_error/script.R b/src/task/metrics/mean_rowwise_error/script.R → src/metrics/mean_rowwise_error/script.R
diff --git a/..._dataset/add_uns_metadata/config.vsh.yaml → ..._dataset/add_uns_metadata/config.vsh.yaml b/..._dataset/add_uns_metadata/config.vsh.yaml → ..._dataset/add_uns_metadata/config.vsh.yaml
diff --git a/...rocess_dataset/add_uns_metadata/script.py → ...rocess_dataset/add_uns_metadata/script.py b/...rocess_dataset/add_uns_metadata/script.py → ...rocess_dataset/add_uns_metadata/script.py
diff --git a/...process_dataset/bootstrap/config.vsh.yaml → ...process_dataset/bootstrap/config.vsh.yaml b/...process_dataset/bootstrap/config.vsh.yaml → ...process_dataset/bootstrap/config.vsh.yaml
diff --git a/src/task/process_dataset/bootstrap/script.py → src/process_dataset/bootstrap/script.py b/src/task/process_dataset/bootstrap/script.py → src/process_dataset/bootstrap/script.py
diff --git a/..._dataset/clean_pseudobulk/config.vsh.yaml → ..._dataset/clean_pseudobulk/config.vsh.yaml b/..._dataset/clean_pseudobulk/config.vsh.yaml → ..._dataset/clean_pseudobulk/config.vsh.yaml
diff --git a/...process_dataset/clean_pseudobulk/script.R → ...process_dataset/clean_pseudobulk/script.R b/...process_dataset/clean_pseudobulk/script.R → ...process_dataset/clean_pseudobulk/script.R
diff --git a/...ataset/compute_pseudobulk/config.vsh.yaml → ...ataset/compute_pseudobulk/config.vsh.yaml b/...ataset/compute_pseudobulk/config.vsh.yaml → ...ataset/compute_pseudobulk/config.vsh.yaml
diff --git a/...cess_dataset/compute_pseudobulk/script.py → ...cess_dataset/compute_pseudobulk/script.py b/...cess_dataset/compute_pseudobulk/script.py → ...cess_dataset/compute_pseudobulk/script.py
diff --git a/...t/convert_h5ad_to_parquet/config.vsh.yaml → ...t/convert_h5ad_to_parquet/config.vsh.yaml b/...t/convert_h5ad_to_parquet/config.vsh.yaml → ...t/convert_h5ad_to_parquet/config.vsh.yaml
diff --git a/...dataset/convert_h5ad_to_parquet/script.py → ...dataset/convert_h5ad_to_parquet/script.py b/...dataset/convert_h5ad_to_parquet/script.py → ...dataset/convert_h5ad_to_parquet/script.py
diff --git a/...rt_kaggle_h5ad_to_parquet/config.vsh.yaml → ...rt_kaggle_h5ad_to_parquet/config.vsh.yaml b/...rt_kaggle_h5ad_to_parquet/config.vsh.yaml → ...rt_kaggle_h5ad_to_parquet/config.vsh.yaml
diff --git a/.../convert_kaggle_h5ad_to_parquet/script.py → .../convert_kaggle_h5ad_to_parquet/script.py b/.../convert_kaggle_h5ad_to_parquet/script.py → .../convert_kaggle_h5ad_to_parquet/script.py
diff --git a/...rocess_dataset/filter_obs/config.vsh.yaml → ...rocess_dataset/filter_obs/config.vsh.yaml b/...rocess_dataset/filter_obs/config.vsh.yaml → ...rocess_dataset/filter_obs/config.vsh.yaml
diff --git a/src/task/process_dataset/filter_obs/script.R → src/process_dataset/filter_obs/script.R b/src/task/process_dataset/filter_obs/script.R → src/process_dataset/filter_obs/script.R
diff --git a/...s_dataset/generate_id_map/config.vsh.yaml → ...s_dataset/generate_id_map/config.vsh.yaml b/...s_dataset/generate_id_map/config.vsh.yaml → ...s_dataset/generate_id_map/config.vsh.yaml
diff --git a/...process_dataset/generate_id_map/script.py → ...process_dataset/generate_id_map/script.py b/...process_dataset/generate_id_map/script.py → ...process_dataset/generate_id_map/script.py
diff --git a/...process_dataset/run_limma/config.vsh.yaml → ...process_dataset/run_limma/config.vsh.yaml b/...process_dataset/run_limma/config.vsh.yaml → ...process_dataset/run_limma/config.vsh.yaml
diff --git a/src/task/process_dataset/run_limma/script.R → src/process_dataset/run_limma/script.R b/src/task/process_dataset/run_limma/script.R → src/process_dataset/run_limma/script.R
diff --git a/src/task/utils/anndata_to_dataframe.py → src/utils/anndata_to_dataframe.py b/src/task/utils/anndata_to_dataframe.py → src/utils/anndata_to_dataframe.py
diff --git a/...workflows/process_dataset/config.vsh.yaml → ...workflows/process_dataset/config.vsh.yaml b/...workflows/process_dataset/config.vsh.yaml → ...workflows/process_dataset/config.vsh.yaml
diff --git a/src/task/workflows/process_dataset/main.nf → src/workflows/process_dataset/main.nf b/src/task/workflows/process_dataset/main.nf → src/workflows/process_dataset/main.nf
diff --git a/...k/workflows/run_benchmark/config.vsh.yaml → src/workflows/run_benchmark/config.vsh.yaml b/...k/workflows/run_benchmark/config.vsh.yaml → src/workflows/run_benchmark/config.vsh.yaml
diff --git a/src/task/workflows/run_benchmark/main.nf → src/workflows/run_benchmark/main.nf b/src/task/workflows/run_benchmark/main.nf → src/workflows/run_benchmark/main.nf
diff --git a/...ws/run_stability_analysis/config.vsh.yaml → ...ws/run_stability_analysis/config.vsh.yaml b/...ws/run_stability_analysis/config.vsh.yaml → ...ws/run_stability_analysis/config.vsh.yaml
diff --git a/.../workflows/run_stability_analysis/main.nf → src/workflows/run_stability_analysis/main.nf b/.../workflows/run_stability_analysis/main.nf → src/workflows/run_stability_analysis/main.nf