Merge pull request #6 from yaseminbridges/5-implement-next-flow-optio…

…n-for-running-ai-marrvel 5 implement next flow option for running ai marrvel
yaseminbridges · Dec 2, 2024 · e8c811e · e8c811e
2 parents e18050e + 53c2597
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diff --git a/README.md b/README.md
@@ -10,6 +10,12 @@ poetry install
 poetry shell
 ```
 
+Alternative install with pip
+
+```shell
+pip install pheval-ai-marrvel
+```
+
 # Configuring a single run:
 
 ## Setting up the input directory
@@ -22,6 +28,7 @@ variant_analysis: True
 gene_analysis: True
 disease_analysis: False
 tool_specific_configuration_options:
+  environment: nextflow # either apptainer/docker/nextflow
 ```
 
 The AI-MARRVEL data dependencies should also be unpacked into the input directory. The overall structure of the input directory should look something like:

diff --git a/config.yaml b/config.yaml
@@ -4,4 +4,4 @@ variant_analysis: True
 gene_analysis: True
 disease_analysis: False
 tool_specific_configuration_options:
-  environment: apptainer # either apptainer or docker
+  environment: nextflow # either apptainer/docker/nextflow