Removed shuffle_by_batch/cell_type mentions in other files

Author: LuLeom

scripts/run_benchmark/wehi_hpc/images.txt

@@ -2,8 +2,6 @@ docker://ghcr.io/openproblems-bio/openproblems/utils/extract_uns_metadata:build_
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/no_integration:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/perfect_integration:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_globally:build_setup_run_hpc
-docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_within_batch:build_setup_run_hpc
-docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/control_methods/shuffle_integration_within_cell_type:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/batchadjust_all_controls:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/batchadjust_one_control:build_setup_run_hpc
 docker://ghcr.io/openproblems-bio/task_cyto_batch_integration/methods/combat:build_setup_run_hpc

src/workflows/run_benchmark/config.vsh.yaml

@@ -83,8 +83,6 @@ dependencies:
   - name: utils/extract_uns_metadata
     repository: op
   - name: control_methods/shuffle_integration_globally
-  - name: control_methods/shuffle_integration_within_batch
-  - name: control_methods/shuffle_integration_within_cell_type
   - name: control_methods/no_integration
   - name: control_methods/perfect_integration
   - name: methods/harmonypy

src/workflows/run_benchmark/main.nf

@@ -10,8 +10,6 @@ workflow auto {
 // construct list of methods and control methods
 methods = [
   shuffle_integration_globally,
-  shuffle_integration_within_batch,
-  shuffle_integration_within_cell_type,
   no_integration,
   perfect_integration,
   combat,