now runs verifybamid for exome

configs/workflow.yaml

@@ -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"

src/run_quac.py

@@ -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")

workflow/rules/common.smk

@@ -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'])

workflow/rules/within_species_contamintation.smk

@@ -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",