update to fit singularity

.github/workflows/build-docker-image.yml

@@ -24,4 +24,4 @@ jobs:
         with:
           file: modules/local/ampliconsuite/Dockerfile
           push: true
-          tags: "quay.io/nf-core/prepareaa:1.0.4"
+          tags: "quay.io/nf-core/prepareaa:1.0.5"

modules/local/ampliconsuite/Dockerfile

@@ -13,26 +13,26 @@ RUN apt-get update && \
     apt-get install -y procps && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
+# Switch back to the default user
+USER $NB_UID
 
-# Install Conda packages with micromamba
+
+# Install Conda packages with micromamba, including Python
 RUN micromamba install --yes --name base -c bioconda -c conda-forge -c mosek \
     bioconda::ampliconsuite=1.2.1 \
     mosek::mosek=10.1.21 && \
     micromamba clean --all --yes
 
+# Assuming AmpliconSuite-pipeline.py is accessible in /opt/conda/bin
+ENV PATH="/opt/conda//bin:${PATH}"
+
 # Append micromamba activation command to .bashrc
 RUN echo "micromamba activate base" >> ~/.bashrc
-RUN echo "export PATH=/opt/conda/bin:\$PATH" >> ~/.bashrc
 
-# Switch back to the default user
-USER $NB_UID
-
-# Start a login bash shell by default
-CMD ["/bin/bash", "-l"]
 
 # Create an entrypoint script
 RUN echo '#!/bin/bash' > /entrypoint.sh && \
-    echo 'source ~/micromamba/etc/profile.d/mamba.sh' >> /entrypoint.sh && \
+    echo 'eval "$(micromamba shell hook --shell bash)"' >> /entrypoint.sh && \
     echo 'micromamba activate base' >> /entrypoint.sh && \
     echo 'exec "$@"' >> /entrypoint.sh && \
     chmod +x /entrypoint.sh

modules/local/ampliconsuite/ampliconsuite.nf

@@ -3,7 +3,7 @@ process AMPLICONSUITE {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container 'nf-core/prepareaa:1.0.2'
+    container 'nf-core/prepareaa:1.0.4'
 
     input:
     tuple val(meta), path(bam)