--- a/Dockerfile	Fri May 15 17:39:30 2026 +0000
+++ b/Dockerfile	Fri May 15 17:50:45 2026 +0000
@@ -1,138 +1,138 @@
-# Multi-stage Dockerfile for SeqSero2S
-# Default build: docker build -t seqsero2s:latest .
-# Test build: docker build --target test -t seqsero2s:test .
-
-# ============================================================================
-# Stage 1: Base image with mambaforge for faster dependency resolution
-# ============================================================================
-FROM condaforge/mambaforge:latest AS base
-
-LABEL maintainer="SeqSero2S Maintainers"
-LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"
-
-# Set environment variables to reduce conda output and ensure non-interactive
-# Disable SSL verification for VPN environments
-ENV CONDA_ALWAYS_YES=true \
-    CONDA_AUTO_UPDATE_CONDA=false \
-    DEBIAN_FRONTEND=noninteractive
-
-# Configure conda to skip SSL verification
-RUN conda config --set ssl_verify false
-
-# ============================================================================
-# Stage 2: Builder - Install all dependencies and SeqSero2S
-# ============================================================================
-FROM base AS builder
-
-# Update base packages and install build essentials
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-    wget \
-    ca-certificates \
-    bash \
-    && apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
-# Create conda environment with all dependencies
-# Using mamba for faster dependency resolution
-RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
-    python>=3 \
-    pip \
-    setuptools \
-    blast>=2.2 \
-    zstd \
-    samtools \
-    bedtools>=2.17 \
-    sra-tools>=2.8 \
-    spades>=3.9 \
-    salmid \
-    bwa>=0.7 \
-    seqtk>=1.3 \
-    stringmlst>=0.6 \
-    mlst>=2.32.2 \
-    perl-list-moreutils \
-    && mamba clean -afy
-
-# Install SeqSero2S from local fork
-WORKDIR /tmp/build/SeqSero2S
-
-# Copy the current build context (the cloned source code) into the container.
-COPY . .
-
-# Install SeqSero2S
-RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
-
-# Apply the stringMLST.py patch inline using 'sed'.
-# This exactly replicates the original python patch script by commenting out the old line and adding the new one.
-RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \
-        sed -i 's|            log = dbPrefix+'\''.log'\''|            # log = dbPrefix+'\''.log'\''\n            log = os.path.join(os.getcwd(), "kmer.log")|g' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \
-        echo "PATCHED: stringMLST.py log path fixed"; \
-    else \
-        echo "SKIP: stringMLST.py not found"; \
-    fi
-
-# ============================================================================
-# Stage 3: Test image - runs validation tests
-# ============================================================================
-FROM builder AS test
-
-# Create test directory
-WORKDIR /test
-
-# Run test commands from the conda recipe
-RUN echo "Running SeqSero2S tests..." && \
-    /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
-    echo "SeqSero2S.py -h: PASSED" && \
-    /opt/conda/envs/seqsero2s/bin/blastn -help && \
-    echo "blastn -help: PASSED" && \
-    /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
-    echo "SalmID.py -h: PASSED" && \
-    /opt/conda/envs/seqsero2s/bin/mlst -h && \
-    echo "mlst -h: PASSED" && \
-    echo "All tests completed successfully!"
-
-# Default command shows test results
-CMD ["echo", "All SeqSero2S tests passed successfully!"]
-
-# ============================================================================
-# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
-# ============================================================================
-FROM condaforge/mambaforge:latest AS dist
-
-# Copy conda environment from builder
-COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
-
-# Update PATH to use the conda environment
-ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \
-    CONDA_DEFAULT_ENV=seqsero2s \
-    CONDA_PREFIX=/opt/conda/envs/seqsero2s
-
-# Install minimal runtime dependencies
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-    ca-certificates \
-    procps \
-    && apt-get clean && \
-    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-# Create working directory
-WORKDIR /data
-
-# Create non-root user for running the application
-RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
-    chown -R seqsero2s:seqsero2s /data
-USER seqsero2s
-
-# Add metadata labels
-LABEL org.opencontainers.image.version="1.1.4" \
-      org.opencontainers.image.authors="LSTUGA" \
-      org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
-      org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
-      org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
-      org.opencontainers.image.licenses="GPL-2.0-or-later" \
-      org.opencontainers.image.title="SeqSero2S" \
-      org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
-
-# No entrypoint or command for dist target
-
-
+# Multi-stage Dockerfile for SeqSero2S
+# Default build: docker build -t seqsero2s:latest .
+# Test build: docker build --target test -t seqsero2s:test .
+
+# ============================================================================
+# Stage 1: Base image with mambaforge for faster dependency resolution
+# ============================================================================
+FROM condaforge/mambaforge:latest AS base
+
+LABEL maintainer="SeqSero2S Maintainers"
+LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"
+
+# Set environment variables to reduce conda output and ensure non-interactive
+# Disable SSL verification for VPN environments
+ENV CONDA_ALWAYS_YES=true \
+    CONDA_AUTO_UPDATE_CONDA=false \
+    DEBIAN_FRONTEND=noninteractive
+
+# Configure conda to skip SSL verification
+RUN conda config --set ssl_verify false
+
+# ============================================================================
+# Stage 2: Builder - Install all dependencies and SeqSero2S
+# ============================================================================
+FROM base AS builder
+
+# Update base packages and install build essentials
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    bash \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Create conda environment with all dependencies
+# Using mamba for faster dependency resolution
+RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
+    python>=3 \
+    pip \
+    setuptools \
+    blast>=2.2 \
+    zstd \
+    samtools \
+    bedtools>=2.17 \
+    sra-tools>=2.8 \
+    spades>=3.9 \
+    salmid \
+    bwa>=0.7 \
+    seqtk>=1.3 \
+    stringmlst>=0.6 \
+    mlst>=2.32.2 \
+    perl-list-moreutils \
+    && mamba clean -afy
+
+# Install SeqSero2S from local fork
+WORKDIR /tmp/build/SeqSero2S
+
+# Copy the current build context (the cloned source code) into the container.
+COPY . .
+
+# Install SeqSero2S
+RUN /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
+
+# Apply the stringMLST.py patch inline using 'sed'.
+# This exactly replicates the original python patch script by commenting out the old line and adding the new one.
+RUN if [ -f "/opt/conda/envs/seqsero2s/bin/stringMLST.py" ]; then \
+        sed -i 's|            log = dbPrefix+'\''.log'\''|            # log = dbPrefix+'\''.log'\''\n            log = os.path.join(os.getcwd(), "kmer.log")|g' /opt/conda/envs/seqsero2s/bin/stringMLST.py && \
+        echo "PATCHED: stringMLST.py log path fixed"; \
+    else \
+        echo "SKIP: stringMLST.py not found"; \
+    fi
+
+# ============================================================================
+# Stage 3: Test image - runs validation tests
+# ============================================================================
+FROM builder AS test
+
+# Create test directory
+WORKDIR /test
+
+# Run test commands from the conda recipe
+RUN echo "Running SeqSero2S tests..." && \
+    /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
+    echo "SeqSero2S.py -h: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/blastn -help && \
+    echo "blastn -help: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
+    echo "SalmID.py -h: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/mlst -h && \
+    echo "mlst -h: PASSED" && \
+    echo "All tests completed successfully!"
+
+# Default command shows test results
+CMD ["echo", "All SeqSero2S tests passed successfully!"]
+
+# ============================================================================
+# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
+# ============================================================================
+FROM condaforge/mambaforge:latest AS dist
+
+# Copy conda environment from builder
+COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
+
+# Update PATH to use the conda environment
+ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \
+    CONDA_DEFAULT_ENV=seqsero2s \
+    CONDA_PREFIX=/opt/conda/envs/seqsero2s
+
+# Install minimal runtime dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    ca-certificates \
+    procps \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Create working directory
+WORKDIR /data
+
+# Create non-root user for running the application
+RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
+    chown -R seqsero2s:seqsero2s /data
+USER seqsero2s
+
+# Add metadata labels
+LABEL org.opencontainers.image.version="1.1.4" \
+      org.opencontainers.image.authors="LSTUGA" \
+      org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.licenses="GPL-2.0-or-later" \
+      org.opencontainers.image.title="SeqSero2S" \
+      org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
+
+# No entrypoint or command for dist target
+
+