main.smk

# Define results this workflow should yield
rule all:
    input:
        expand(
            "{runid}_results/fastqc/{id}/{id}_{orientation}_fastqc.{extension}",
            runid=config["samples"]["runid"],
            id=config["samples"]["barcodes"],
            orientation=["R1", "R2"],
            extension=["html", "zip"],
        ),
        expand(
            "{runid}_results/genome_coverage/{id}/{id}.mosdepth.{files}.txt",
            runid=config["samples"]["runid"],
            id=config["samples"]["barcodes"],
            files=["global.dist", "summary"],
        ),
        expand(
            "{runid}_results/seqtools/{id}/tumorSV_annotated_processed.txt",
            runid=config["samples"]["runid"],
            id=config["samples"]["barcodes"],
        ),


# Combine fastq files for same sample from different barcodes and lanes
include: "src/combine_fastq.smk"
# Run fastqc QC analysis on combined fastq files
include: "src/fastqc.smk"
# Trim adapters and fix MGI fastq header with fastp
include: "src/fastp.smk"
# Align reads to reference genome using the super fast bwa-mem2
include: "src/bwa_mem2.smk"
# Mark duplicated reads using GATK4 Spark
include: "src/mark_duplicates.smk"
# Calculate Genome coverage with bedtools
include: "src/genome_coverage.smk"
# CNV calling using Manta
include: "src/manta.smk"
# Annotation using SnpEff
include: "src/snpeff.smk"
# Annotation using simple_sv_annotation
include: "src/simple_sv_annotation.smk"
# Melt vcf with seqtools
include: "src/seqtools.smk"
# Collect insert size metrics using GATK4 Picard - no output rule
include: "src/insert_size_metrics.smk"
# CNV calling using BreakDancer - no output rule
include: "src/breakdancer.smk"
# CNV calling using Lumpy - no output rule
include: "src/lumpy.smk"
# CNV calling using Pindel - not recommended to run on WGS
include: "src/pindel.smk"