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def get_svd(wildcards):
if EXOME_MODE:
return expand(f"{config['datasets']['verifyBamID']['svd_dat_exome']}.{{ext}}", ext=["bed", "mu", "UD"])
return expand(f"{config['datasets']['verifyBamID']['svd_dat_wgs']}.{{ext}}", ext=["bed", "mu", "UD"])
bam=PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam",
bam_index=PROJECT_PATH / "{sample}" / "bam" / "{sample}.bam.bai",
ref_genome=config["datasets"]["ref"],
ancestry=protected(OUT_DIR / "{sample}" / "qc" / "verifyBamID" / "{sample}.Ancestry"),
selfsm=protected(OUT_DIR / "{sample}" / "qc" / "verifyBamID" / "{sample}.selfSM"),
"Running VerifyBamID to detect within-species contamination. sample: {wildcards.sample}"
conda:
str(WORKFLOW_PATH / "configs/env/verifyBamID.yaml")
params:
svd_prefix=lambda wildcards, input: input["svd"][0].replace(Path(input["svd"][0]).suffix, ""),
out_prefix=lambda wildcards, output: output["ancestry"].replace(".Ancestry", ""),
sanity_check="--DisableSanityCheck" if is_testing_mode() else "",
threads: config["resources"]["verifybamid"]["no_cpu"]
verifybamid2 {params.sanity_check} \
--Reference {input.ref_genome} \
--BamFile {input.bam} \