Merge branch 'main' of github.com:adamd3/BactSeq

- Add conda environment activation with CONDA_DEFAULT_ENV

Author: adamd3

.github/workflows/ci.yml

@@ -31,7 +31,7 @@ jobs:
             aligner: "kallisto"
             test_type: "single-end"
           # Test with latest Nextflow version
-          - NXF_VER: "23.10.1"
+          - NXF_VER: "25.04.0"
             NXF_EDGE: ""
             aligner: "bwa"
             test_type: "single-end"

Dockerfile

@@ -6,11 +6,10 @@ COPY environment.yml /app
 
 RUN conda env create -f environment.yml
 
-RUN echo "conda activate bact_seq-1.0.0" >> ~/.bashrc
+# Set conda environment as default
+ENV CONDA_DEFAULT_ENV=bact_seq-1.0.0
 ENV PATH=/opt/conda/envs/bact_seq-1.0.0/bin:$PATH
 
 SHELL ["/bin/bash", "-c"]
 
 COPY . /app
-
-ENTRYPOINT ["bash", "-c", "source activate bact_seq-1.0.0 && exec bash"]