⛓️Predefined Workflows

COSAP users don't need to create a custom pipeline if they are not tweaking parameters. The DefaultPipeline provides an interface for creating a DNA-SEQ analysis pipeline with algorithm combinations.

An example DNAPipelineInput looks like this.

from cosap import DNAPipelineInput, DNAPipeline

dna_pipe_input = DNAPipelineInput(
    ANALYSIS_TYPE = "somatic",
    WORKDIR = "your_workdir",
    NORMAL_SAMPLE = ("sample_1.fastq", "sample_2.fastq"),
    TUMOR_SAMPLES = [("tumor1_1.fastq", "tumor_1_2.fastq"), ("tumor2_1.fastq", "tumor_2_2.fastq")],
    BED_FILE = None,
    MAPPERS = ["bwa2", "bowtie"],
    VARIANT_CALLERS = ["mutect", "octopus"],
    NORMAL_SAMPLE_NAME = "your_normal_sample_name",
    TUMOR_SAMPLE_NAME = "your_tumor_sample_name",
    BAM_QC = "qualimap",
    ANNOTATORS = "cancervar",
    GVCF = True,
    MSI = True,
    GENEFUSION = True
)

You can then run the DNAPipeline as

dna_pipeline = DNAPipeline(dna_pipeline_input)
dna_pipeline.run_pipeline()