clintval

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

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

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

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

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

class MethodType:
    """A Python-equivalent method type that binds type arguments to the calling class."""

    def __init__(self, func: Callable, obj: object) -> None:
        """Initialize this method with the calling class and function."""
        self.__func__ = func
        self.__self__ = obj
        self._generic_classmethod = False

    def __call__(self, *args: object, **kwargs: object) -> object:

clintval

def is_classmethod(method: FunctionType) -> bool:
    """Determine if a method is a classmethod or not by searching for a classmethod sentinel."""
    bound_to = getattr(method, "__self__", None)
    if not isinstance(bound_to, type):
        return False
    name = method.__name__
    for clazz in bound_to.__mro__:
        descriptor = vars(clazz).get(name)
        if descriptor is not None:
            return isinstance(descriptor, classmethod)

clintval

{
cat <<- EOM
#!/usr/bin/env sh
set -e

PROP_OPTS=()
MEM_OPTS=()
PASS_ARGS=()
DEFAULT_MEM_OPTS=('-Xms512m' '-XX:+AggressiveHeap')

clintval

#!/bin/bash

# Attempts to compile the groovy present in nextflow/lib/ with the groovy compiler and nextflow
# libararies properly linked (because they dont live in a place groovy can find them by default.)
#
# Must have a conda env with nextflow and groovy installed in order for this script to work. 

SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )

clintval

# Convert DOT graph data into a terminal-ready visualization
function idot {
  dot \
      -Tpng -Gdpi=300 \
      -Efontsize=18 -Efontname=sans -Nfontname=sans \
      -Gbgcolor=black -Gcolor=white -Ecolor=white -Efontcolor=white -Ncolor=white -Nfontcolor=white \
    | convert -trim -bordercolor black -border 20 -transparent black -resize "60%" - - \
    | imgcat # Or swap with your favorite terminal image viewer
}