Add new module sentieoncli/dnascopelongread

modules/nf-core/sentieoncli/dnascopelongread/Dockerfile

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+FROM debian:stable-20260112-slim AS downloader
+
+ARG SENTIEON_VERSION=202503.02
+ARG SENTIEON_CLI_VERSION=1.5.2
+
+RUN test -n "$SENTIEON_VERSION"
+
+LABEL container.base.image="debian:stable-20260112-slim" \
+    software.version="${SENTIEON_VERSION}" \
+    software.website="https://www.sentieon.com/"
+
+# Download the software from the permalink
+RUN apt-get update && apt-get install -y curl
+RUN mkdir -p /opt/sentieon/
+RUN curl -L "https://s3.amazonaws.com/sentieon-release/software/sentieon-genomics-${SENTIEON_VERSION}.tar.gz" | tar -zxf - -C /opt/sentieon/
+
+# Build gnuplot
+RUN apt-get update && apt-get install -y curl make gcc gzip libgd-dev libcairo2-dev libpango1.0-dev && \
+    curl -L "https://downloads.sourceforge.net/project/gnuplot/gnuplot/6.0.2/gnuplot-6.0.2.tar.gz" | \
+    tar -zxf - && \
+    cd gnuplot-6.0.2 && \
+    ./configure && \
+    make install
+
+# Build the container
+FROM debian:stable-20260112-slim
+ENV SENTIEON_VERSION=$SENTIEON_VERSION
+
+COPY --from=downloader /opt/sentieon/sentieon-genomics-${SENTIEON_VERSION} /opt/sentieon/sentieon-genomics-${SENTIEON_VERSION}
+COPY --from=downloader /usr/local/bin/gnuplot /usr/local/bin/gnuplot
+COPY --from=downloader /usr/local/libexec/gnuplot/6.0/gnuplot_x11 /usr/local/libexec/gnuplot/6.0/gnuplot_x11
+COPY --from=downloader /usr/local/share/gnuplot/6.0 /usr/local/share/gnuplot/6.0
+CMD ["/bin/bash"]
+
+# Install jemalloc as the recommended memory allocation tool, see https://support.sentieon.com/appnotes/jemalloc/
+# Install procps for process monitoring
+RUN apt-get update && apt-get install -y \
+    libjemalloc2 \
+    procps \
+    libgd-dev \
+    libcairo2-dev \
+    libpango1.0-dev \
+    locales \
+    git \
+    curl \
+    ca-certificates \
+    bzip2 \
+    isal \
+    && sed -i 's/^# *\(en_US.UTF-8\)/\1/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && echo "LANG=en_US.UTF-8" | tee /etc/default/locale \
+    && rm -rf /var/lib/apt/lists/* /var/cache/apt/archives
+
+ENV LC_ALL=en_US.UTF-8
+ENV SENTIEON_INSTALL_DIR=/opt/sentieon/sentieon-genomics-$SENTIEON_VERSION
+ENV PATH=${SENTIEON_INSTALL_DIR}/bin:${PATH}
+ENV LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so.2
+
+ARG MICROMAMBA_VERSION=1.5.8-0
+ARG MICROMAMBA_ARCH=linux-64
+ENV MAMBA_ROOT_PREFIX=/opt/conda
+ENV PATH=${MAMBA_ROOT_PREFIX}/bin:${PATH}
+
+RUN set -eux; \
+    mkdir -p "$MAMBA_ROOT_PREFIX"; \
+    curl -fsSL "https://github.com/mamba-org/micromamba-releases/releases/download/${MICROMAMBA_VERSION}/micromamba-${MICROMAMBA_ARCH}" -o /usr/local/bin/micromamba; \
+    chmod 755 /usr/local/bin/micromamba
+
+ARG SENTIEON_CLI_REPO=https://github.com/Sentieon/sentieon-cli.git
+
+RUN set -eux; \
+    micromamba create -y -n sentieon-cli -c conda-forge -c bioconda \
+    python=3.11 \
+    pip=24.0 \
+    samtools=1.22 \
+    bcftools=1.22 \
+    htslib=1.22 \
+    pysam=0.23.0 \
+    click=8.1.7 \
+    pyyaml=6.0.1 \
+    pandas=2.2.2 \
+    requests=2.32.3 \
+    bedtools=2.31.1 \
+    mosdepth=0.3.12 \
+    hificnv=1.0.1 \
+    packaging=24.0 \
+    colorlog=6.9.0 \
+    importlib_resources=6.4.5; \
+    micromamba clean --all --yes
+
+RUN set -eux; \
+    micromamba run -n sentieon-cli pip install --no-deps "git+${SENTIEON_CLI_REPO}@${SENTIEON_CLI_VERSION}";
+
+ENV SENTIEON_CLI_ENV=${MAMBA_ROOT_PREFIX}/envs/sentieon-cli
+ENV PATH=${SENTIEON_CLI_ENV}/bin:${MAMBA_ROOT_PREFIX}/bin:${SENTIEON_INSTALL_DIR}/bin:${PATH}
+ENV CONDA_DEFAULT_ENV=sentieon-cli
+
+# A default jemalloc configuration that should work well for most use-cases, see http://jemalloc.net/jemalloc.3.html
+ENV MALLOC_CONF=metadata_thp:auto,background_thread:true,dirty_decay_ms:30000,muzzy_decay_ms:30000

modules/nf-core/sentieoncli/dnascopelongread/main.nf

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+process SENTIEONCLI_DNASCOPELONGREAD {
+
+    tag "${meta.id}"
+    label 'process_high'
+    label 'sentieon'
+
+    secret 'SENTIEON_LICENSE_BASE64'
+
+    container "docker.io/clinicalgenomicslund/dnascope-longread:1.5.2"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(diploid_intervals_bed), path(haploid_intervals_bed)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(model_bundle)
+    tuple val(meta5), path(dbsnp)
+    tuple val(meta6), path(dbsnp_tbi)
+    tuple val(meta7), path(pop_vcf)
+    tuple val(meta8), path(pop_vcf_tbi)
+    tuple val(meta9), path(cnv_excluded_regions)
+    val tech
+    val emit_snvs
+    val emit_gvcf
+    val emit_svs
+    val emit_cnvs
+    val emit_qc
+
+    output:
+    tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: vcf_tbi, optional: true
+    tuple val(meta), path("${prefix}.g.vcf.gz"), emit: gvcf, optional: true
+    tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi, optional: true
+    tuple val("${task.process}"), val("sentieon-cli"), eval("sentieon-cli --version"), topic: versions, emit: versions_sentieon_cli
+    tuple val("${task.process}"), val("sentieon"), eval("sentieon driver --version 2>&1 | sed -e 's/sentieon-genomics-//g'"), topic: versions, emit: versions_sentieon
+    tuple val("${task.process}"), val('bedtools'), eval("bedtools --version | sed -e 's/bedtools v//g'"), topic: versions, emit: versions_bedtools
+    tuple val("${task.process}"), val("samtools"), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
+    tuple val("${task.process}"), val("bcftools"), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def diploid_bed_cmd = diploid_intervals_bed ? "--diploid_bed ${diploid_intervals_bed}" : ""
+    def haploid_bed_cmd = haploid_intervals_bed ? "--haploid_bed ${haploid_intervals_bed}" : ""
+    def dbsnp_cmd = dbsnp ? "--dbsnp ${dbsnp}" : ""
+    def popvcf_cmd = pop_vcf ? "--pop_vcf ${pop_vcf}" : ""
+    def gvcf_cmd = emit_gvcf ? "--gvcf" : ""
+    def vcf_cmd = emit_snvs ? "" : "--skip_small_variants"
+    def sv_cmd = emit_svs ? "" : "--skip_svs"
+    def cnv_cmd = emit_cnvs ? "" : "--skip_cnv"
+    def cnv_excluded_regions_cmd = cnv_excluded_regions ? "" : "--skip_mosdepth"
+    def qc_cmd = emit_qc ? "" : "--skip_mosdepth"
+    """
+    sentieon-cli dnascope-longread \\
+        ${args} \\
+        --cores ${task.cpus} \\
+        --tech ${tech} \\
+        -r ${fasta} \\
+        -i ${bam} \\
+        -m ${model_bundle} \\
+        ${diploid_bed_cmd} \\
+        ${haploid_bed_cmd} \\
+        ${dbsnp_cmd} \\
+        ${popvcf_cmd} \\
+        ${gvcf_cmd} \\
+        ${vcf_cmd} \\
+        ${sv_cmd} \\
+        ${cnv_cmd} \\
+        ${qc_cmd} \\
+        ${cnv_excluded_regions_cmd} \\
+        --skip_mosdepth \\
+        --skip_cnv \\
+        --skip_svs \\
+        ${prefix}.vcf.gz
+   """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    echo "" | gzip > ${prefix}.g.vcf.gz
+    touch ${prefix}.g.vcf.gz.tbi
+    """
+}