rename task

CHANGELOG.md

@@ -1,10 +1,10 @@
-# task-dge-perturbation-prediction 0.1.0
+# task_perturbation_prediction 1.0.0
 
-Initial release of the DGE Perturbation Prediction task. Initial components:
+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`: DGE perturbation prediction methods: random_forest.
-* `src/task/metrics`: Evaluation metrics: mean_rowwise_error.
+* `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.
 
 

README.md

@@ -10,7 +10,7 @@ Predicting how small molecules change gene expression in different cell
 types.
 
 Path to source:
-[`src/task`](https://github.com/openproblems-bio/task-dge-perturbation-prediction/tree/main/src/task)
+[`src/task`](https://github.com/openproblems-bio/task_perturbation_prediction/tree/main/src/task)
 
 ## Installation
 
@@ -27,9 +27,9 @@ To add a method to the repository, follow the instructions in the `scripts/add_a
 To get started, you can run the following commands:
 
 ```bash
-git clone git@github.com:openproblems-bio/task-dge-perturbation-prediction.git
+git clone git@github.com:openproblems-bio/task_perturbation_prediction.git
 
-cd task-dge-perturbation-prediction
+cd task_perturbation_prediction
 
 # download resources
 scripts/download_resources.sh

_viash.yaml

@@ -7,8 +7,8 @@ config_mods: |
   .functionality.version := 'dev'
   .functionality.arguments[.multiple == true].multiple_sep := ';'
   .platforms[.type == 'docker'].target_registry := 'ghcr.io'
-  .platforms[.type == 'docker'].target_organization := 'openproblems-bio/task-perturbation-prediction'
-  .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/task-perturbation-prediction'
+  .platforms[.type == 'docker'].target_organization := 'openproblems-bio/task_perturbation_prediction'
+  .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/task_perturbation_prediction'
   .platforms[.type == "nextflow"].directives.tag := "$id"
   .platforms[.type == "nextflow"].auto.simplifyOutput := false
   .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }

scripts/render_readme.sh

@@ -7,5 +7,5 @@ set -e
 ../openproblems-v2/target/docker/common/create_task_readme/create_task_readme \
   --task "dge_perturbation_prediction" \
   --task_dir "src/task" \
-  --github_url "https://github.com/openproblems-bio/task-dge-perturbation-prediction/tree/main/" \
+  --github_url "https://github.com/openproblems-bio/task_perturbation_prediction/tree/main/" \
   --output "README.md"

scripts/run_benchmark_tw.sh

@@ -20,7 +20,7 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-tw launch https://github.com/openproblems-bio/task-dge-perturbation-prediction.git \
+tw launch https://github.com/openproblems-bio/task_perturbation_prediction.git \
   --revision main_build \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \

scripts/run_benchmark_tw_traens.sh

@@ -18,8 +18,8 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-tw launch https://github.com/openproblems-bio/task-dge-perturbation-prediction.git \
-  --revision fix_trafo_ens_build \
+tw launch https://github.com/openproblems-bio/task_perturbation_prediction.git \
+  --revision suggestions_elior_build \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \
   --workspace 53907369739130 \

scripts/run_layert_tw.sh

@@ -12,7 +12,7 @@ rename_keys: "de_train_h5ad:de_train_h5ad,de_test_h5ad:de_test_h5ad,id_map:id_ma
 settings: '{"layer": "t"}'
 HERE
 
-tw launch https://github.com/openproblems-bio/task-dge-perturbation-prediction.git \
+tw launch https://github.com/openproblems-bio/task_perturbation_prediction.git \
   --revision main_build \
   --pull-latest \
   --main-script target/nextflow/workflows/run_benchmark/main.nf \

scripts/run_stability_tw.sh

@@ -11,7 +11,7 @@ output_state: "state.yaml"
 publish_dir: "$publish_dir"
 HERE
 
-tw launch https://github.com/openproblems-bio/task-dge-perturbation-prediction.git \
+tw launch https://github.com/openproblems-bio/task_perturbation_prediction.git \
   --revision main_build \
   --pull-latest \
   --main-script target/nextflow/workflows/run_stability_analysis/main.nf \

scripts/sync_results.sh

@@ -15,4 +15,4 @@ aws s3 sync \
 runid=run_2024-06-01_00-03-09; aws s3 sync \
   output/benchmark_results/${runid}/ \
   s3://openproblems-data/resources/dge_perturbation_prediction/results/${runid}/ \
-  --delete --dryrun
+  --delete --dryrun

src/common/create_component/script.py

@@ -6,7 +6,7 @@
 
 ## VIASH START
 par = {
-  "task": "DGE Perturbation Prediction",
+  "task": "Perturbation Prediction",
   "type": "method",
   "language": "python",
   "name": "new_comp",

src/task/api/task_info.yaml

@@ -17,9 +17,9 @@ readme: |
   To get started, you can run the following commands:
 
   ```bash
-  git clone git@github.com:openproblems-bio/task-dge-perturbation-prediction.git
+  git clone git@github.com:openproblems-bio/task_perturbation_prediction.git
 
-  cd task-dge-perturbation-prediction
+  cd task_perturbation_prediction
   
   # download resources
   scripts/download_resources.sh

src/task/process_dataset/add_uns_metadata/config.vsh.yaml

@@ -7,7 +7,7 @@ functionality:
       label: Add metadata
       summary: Add metadata to the pseudobulked data
       description: |
-        Add metadata to the pseudobulked single-cell dataset for the DGE regression task.
+        Add metadata to the pseudobulked single-cell dataset for the perturbation regression task.
   arguments:
     - name: --input
       type: file

src/task/process_dataset/compute_pseudobulk/config.vsh.yaml

@@ -7,7 +7,7 @@ functionality:
       label: Pseudobulk
       summary: Compute pseudobulk data
       description: |
-        Compute pseudobulk data for the DGE regression task.
+        Compute pseudobulk data for the perturbation regression task.
   arguments:
     - name: --input
       type: file

src/task/process_dataset/run_limma/config.vsh.yaml

@@ -7,7 +7,7 @@ functionality:
       label: Limma
       summary: Run limma
       description: |
-        Run limma for the DGE regression task.
+        Run limma for the parturbation regression task.
   arguments:
     - name: --input
       type: file