dodona-nextflow.dockerfile

FROM amazoncorretto:21-al2023-headless
ARG NXF_VER=24.10.2
ARG FASTQC_VER=0.11.9
ARG MULTIQC_VER=1.25.2
ARG TRIMMOMATIC_VER=0.39

RUN chmod 711 /mnt \
    && dnf install -y --setopt=install_weak_deps=False --best procps-ng shadow-utils which jq perl python3-pip python3-setuptools unzip \
    && dnf clean all \
    && useradd -m runner

USER runner

ENV PATH="/home/runner/bin:/home/runner/.local/bin:$PATH"
ENV NXF_VER=${NXF_VER}
ENV NXF_HOME="/home/runner/.nextflow"
ENV NXF_OFFLINE="true"
ENV FASTQC_HOME="/home/runner/.fastqc"

RUN <<EOF
    set -e
    mkdir -p ~/workdir
    mkdir ~/bin
    pushd ~/bin
    curl -fLO "https://github.com/nextflow-io/nextflow/releases/download/v$NXF_VER/nextflow"
    chmod +x nextflow
    mkdir -p "$NXF_HOME/framework/$NXF_VER"
    curl -fLo "$NXF_HOME/framework/$NXF_VER/nextflow-$NXF_VER-one.jar" "https://www.nextflow.io/releases/v$NXF_VER/nextflow-$NXF_VER-one.jar"
    curl -fLO 'https://repo1.maven.org/maven2/org/codenarc/CodeNarc/3.5.0-groovy-4.0/CodeNarc-3.5.0-groovy-4.0-all.jar'
    curl -fLO 'https://github.com/awslabs/linter-rules-for-nextflow/releases/download/v0.1.0/linter-rules-0.1.jar'
    curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-api/1.7.36/slf4j-api-1.7.36.jar'
    curl -fLO 'https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/1.7.36/slf4j-simple-1.7.36.jar'
    printf 'java -Dorg.slf4j.simpleLogger.defaultLogLevel=error -classpath "$HOME/bin/linter-rules-0.1.jar:$HOME/bin/CodeNarc-3.5.0-groovy-4.0-all.jar:$HOME/bin/slf4j-api-1.7.36.jar:$HOME/bin/slf4j-simple-1.7.36.jar" "org.codenarc.CodeNarc" "$@"' > nextflow-linter
    chmod +x nextflow-linter
    popd
    TMPFILE=$(mktemp)
    curl -fLo "$TMPFILE" "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v$FASTQC_VER.zip"
    mkdir "$FASTQC_HOME"
    ln -s "$FASTQC_HOME" "$FASTQC_HOME/FastQC"
    unzip "$TMPFILE" -d "$FASTQC_HOME"
    rm "$TMPFILE" "$FASTQC_HOME/FastQC"
    chmod +x "$FASTQC_HOME/fastqc"
    ln -s "$FASTQC_HOME/fastqc" "$HOME/bin/fastqc"
    pip3 install --no-cache-dir "multiqc==$MULTIQC_VER"
    curl -fLo "$TMPFILE" "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-$TRIMMOMATIC_VER.zip"
    TMPFOLDER=$(mktemp -d)
    unzip "$TMPFILE" -d "$TMPFOLDER/"
    mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/trimmomatic-$TRIMMOMATIC_VER.jar" "$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar"
    mv "$TMPFOLDER/Trimmomatic-$TRIMMOMATIC_VER/adapters/"* "$HOME/workdir"
    rm -r "$TMPFILE" "$TMPFOLDER"
    printf "#!/bin/sh\njava -jar \"$HOME/bin/trimmomatic-$TRIMMOMATIC_VER.jar\"" > "$HOME/bin/trimmomatic"
    chmod +x "$HOME/bin/trimmomatic"
EOF

WORKDIR /home/runner/workdir

COPY main.sh /main.sh