clintval

def dna_sequence_from_DAS(build: str, chrom: str, start: int, end: int) -> str:
    """
    Return the DNA sequence along an interval for a reference sequence build.

    Uses the DAS web server.

    Args:
        build: The UCSC genome build.
        chrom: The reference sequence name.
        start: The 1-based start locus.

clintval

FROM debian:bookworm-20250113-slim AS base

ENV LANG=C.UTF-8

RUN apt-get update \
    && apt-get install -y --no-install-recommends \
        build-essential \
        cmake \
        git \
        gnupg \

clintval

################################################################################
# Update and install OS packages
# https://docs.anaconda.com/anaconda/install/silent-mode/#linux-macos
################################################################################
RUN curl --location --fail --remote-name \
        https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh \
    && bash Miniforge3-Linux-x86_64.sh -b -p /opt/conda -u \
    && rm Miniforge3-Linux-x86_64.sh

###############################################################################

clintval

process FASTQC {
    container "community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29"

    input:
    tuple val(meta), path(fastqs, arity: "1..*")

    output:
    path("*.zip"), topic: "for_multiqc"
    tuple val(meta), path("*.html"), emit: reports, topic: "per_sample"
    tuple val(meta), path("*.zip"), emit: metrics, topic: "per_sample"

clintval

rule all:
    input:
        #######################################################################
        #
        # Pipeline #1 Flow cell QC and Demultiplexing
        #
        #######################################################################
        # check_illumina_directory
        f'{run_output}/logs/CheckIlluminaDirectory.log',
        # collect_illumina_lane_metrics