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Commit a3a66de2 authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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now runs verifybamid for exome

parent 80e9da30
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1 merge request!1QuaC - First major review
......@@ -10,4 +10,5 @@ somalier:
goleft:
tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/goleft/0.2.4/goleft"
verifyBamID:
svd_dat: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/verifyBamID/VerifyBamID-2.0.1/resource/1000g.phase3.100k.b38.vcf.gz.dat"
svd_dat_wgs: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/verifyBamID/VerifyBamID-2.0.1/resource/1000g.phase3.100k.b38.vcf.gz.dat"
svd_dat_exome: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/verifyBamID/VerifyBamID-2.0.1/resource/exome/1000g.phase3.10k.b38.exome.vcf.gz.dat"
......@@ -38,7 +38,7 @@ def create_snakemake_command(args):
cmd = [
"snakemake",
f"--snakefile '{snakefile_path}'",
f"--config modules='{args.modules}' project_name='{args.project_name}' ped='{args.pedigree}' out_dir='{args.outdir}' log_dir='{args.log_dir}'",
f"--config modules='{args.modules}' project_name='{args.project_name}' ped='{args.pedigree}' out_dir='{args.outdir}' log_dir='{args.log_dir}' exome={args.exome}",
f"--restart-times {args.rerun_failed}",
"--use-conda",
f"--profile '{snakemake_profile_dir}'",
......@@ -149,6 +149,11 @@ if __name__ == "__main__":
default="all",
metavar="",
)
WORKFLOW.add_argument(
"--exome",
action="store_true",
help="Flag to run in exome mode",
)
############ Args for QuaC wrapper tool ############
WRAPPER = PARSER.add_argument_group("QuaC wrapper options")
......
......@@ -59,6 +59,7 @@ OUT_DIR = Path(config['out_dir'])
PROJECT_NAME = config['project_name']
MODULES_TO_RUN = modules_to_run(config['modules'])
PEDIGREE_FPATH = config['ped']
EXOME_MODE = config['exome']
#### configs from configfile ####
PROJECTS_PATH = Path(config['projects_path'])
......
......@@ -2,14 +2,21 @@ TARGETS_CONTAMINATION = [
get_targets('verifybamid', SAMPLES) if {'all', 'verifybamid'}.intersection(MODULES_TO_RUN) else [],
]
def get_svd(wildcards):
if EXOME_MODE:
return expand(f"{config['verifyBamID']['svd_dat_exome']}.{{ext}}",
ext=['bed', 'mu', 'UD'])
else:
return expand(f"{config['verifyBamID']['svd_dat_wgs']}.{{ext}}",
ext=['bed', 'mu', 'UD'])
rule verifybamid:
input:
bam = PROJECTS_PATH / PROJECT_NAME / "analysis" / "{sample}" / "bam" / "{sample}.bam",
bam_index = PROJECTS_PATH / PROJECT_NAME / "analysis" / "{sample}" / "bam" / "{sample}.bam.bai",
ref_genome = config['ref'],
svd = expand(f"{config['verifyBamID']['svd_dat']}.{{ext}}",
ext=['bed', 'mu', 'UD'])
svd = get_svd
output:
ancestry = OUT_DIR / "verifyBamID/{sample}.Ancestry",
selfsm = OUT_DIR / "verifyBamID/{sample}.selfSM",
......
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