Extend cell cycle conservation support for zebrafish and C. elegans

CONTRIBUTING.md

@@ -146,3 +146,18 @@ To run the benchmark, you can use the following command:
 ```bash
 scripts/run_benchmark/run.sh
 ```
+
+## Debugging nf-tower runs
+
+The actual benchmark is run on the [nf-tower platform](https://cloud.seqera.io/orgs/openproblems-bio/workspaces/openproblems-bio/watch).
+You can find runs related to the batch integration by filtering for `label:task_batch_integration`, selecting a specific run and browsing the outputs.
+
+For debugging purposes, you can download the output of a task run from nf-tower following command:
+
+```bash
+common/scripts/fetch_task_run \
+  --input s3://openproblems-work/work/<process ID>\
+  --output temp_output
+```
+
+You can find the process ID under the "Work directory" section of the Task details.

src/metrics/cell_cycle_conservation/config.vsh.yaml

@@ -28,7 +28,7 @@ info:
         doi: 10.1038/s41592-021-01336-8
       links:
         homepage: https://scib.readthedocs.io/en/latest/
-        documentation: https://scib.readthedocs.io/en/latest/api/scib.metrics.silhouette_batch.html
+        documentation: https://scib.readthedocs.io/en/latest/api/scib.metrics.cell_cycle.html
         repository: https://github.com/theislab/scib
       min: 0
       max: 1
@@ -43,7 +43,7 @@ engines:
     setup:
       - type: python
         pypi:
-          - scib==1.1.5
+          - git+https://github.com/theislab/scib.git@extend_cell_cycle_genes
 runners:
   - type: executable
   - type: nextflow

src/metrics/kbet/config.vsh.yaml

@@ -50,7 +50,7 @@ engines:
         github: theislab/kBET
       - type: python
         pypi:
-          - scib==1.1.5
+          - scib==1.1.6
           - rpy2>=3
           - anndata2ri
           - scipy<=1.13