updated Dockerfile

Author: VictorDidier

Dockerfile

@@ -1,7 +1,33 @@
+# Use the official micromamba image as a base
 FROM mambaorg/micromamba:latest
-COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yaml
-RUN micromamba install -y -n base -f /tmp/env.yaml && \
-    micromamba clean --all --yes
+LABEL maintainer="Victor Perez"
+
+# Set the base layer for micromamba and copy the environment file
+USER root
+COPY environment.yml .
+# Update package manager and install essential build tools procps is required for Nextflow/nf-core
+RUN apt-get update -qq && apt-get install -y \
+    build-essential \
+    ffmpeg \
+    libsm6 \
+    libxext6 \
+    procps
+
+# Set the environment variable for the root prefix
+ARG MAMBA_ROOT_PREFIX=/opt/conda
+
+# Add /opt/conda/bin to the PATH
+ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
+
+# Install dependencies with micromamba, clean afterwards
+RUN micromamba env create -f environment.yml \
+    && micromamba clean --all --yes
+
+# Add environment to PATH
 ENV PATH="${PATH}:/opt/conda/bin"
+
+# Set the working directory
 WORKDIR /staging
+
+# Copy contents of the folder to the working directory
 COPY . .