Merge pull request #341 from Bond-009/nextflow

Add Dockerfile for Nextflow judge

.github/workflows/build.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        image: [assembly, bash, c, compilers, csharp, docker, haskell, html, java, java21, nodejs, postgres, prolog, python, r, scheme, sqlite, tested]
+        image: [assembly, bash, c, compilers, csharp, docker, haskell, html, java, java21, nextflow, nodejs, postgres, prolog, python, r, scheme, sqlite, tested]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master

.github/workflows/lint.yml

@@ -8,12 +8,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        image: [assembly, bash, c, compilers, csharp, docker, haskell, html, java, java21, nodejs, postgres, prolog, python, r, scheme, sqlite, tested]
+        image: [assembly, bash, c, compilers, csharp, docker, haskell, html, java, java21, nextflow, nodejs, postgres, prolog, python, r, scheme, sqlite, tested]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: jbergstroem/hadolint-gh-action@v1
         with:
           dockerfile: dodona-${{ matrix.image }}.dockerfile
           error_level: 1
-          config_file: hadolint.yml
+          config_file: hadolint.yml

dodona-nextflow.dockerfile

@@ -0,0 +1,57 @@
+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