switches to cli to supply projects_path

configs/workflow.yaml

-projects_path: "/data/project/worthey_lab/projects/"
-# project_names: "MuscDyst_SU_MAlexander,CF_CFF_PFarrell,CF_TLOAF_PFarrell,EDS3_unkn_DGreenspan,UDN_Phase1_EAWorthey"
-# project_name: "CF_CFF_PFarrell"
 ref: "/data/project/worthey_lab/datasets_central/human_reference_genome/processed/GRCh38/no_alt_rel20190408/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
 somalier:
     tool: "/data/project/worthey_lab/projects/experimental_pipelines/mana/tools/somalier/0.2.12/somalier"

src/run_quac.py

@@ -37,6 +37,7 @@ def create_snakemake_command(args):
     quac_configs = {
         "modules": args.modules,
         "project_name": args.project_name,
+        "projects_path": args.projects_path,
         "ped": args.pedigree,
         "out_dir": str(Path(args.outdir) / args.project_name),
         "log_dir": args.log_dir,
@@ -137,6 +138,15 @@ if __name__ == "__main__":
         help="Project name",
         metavar="",
     )
+
+    PROJECT_PATH_DEFAULT = "/data/project/worthey_lab/projects/"
+    WORKFLOW.add_argument(
+        "--projects_path",
+        help="Path where all projects are hosted. Don't include project name here.",
+        default=PROJECT_PATH_DEFAULT,
+        type=lambda x: is_valid_dir(PARSER, x),
+        metavar="",
+    )
     WORKFLOW.add_argument(
         "--pedigree",
         help="Pedigree filepath. Must correspond to the project supplied via --project_name",

workflow/rules/common.smk

@@ -57,13 +57,13 @@ def get_targets(tool_name, samples=None):
 #### configs from cli ####
 OUT_DIR = Path(config['out_dir'])
 PROJECT_NAME = config['project_name']
+PROJECTS_PATH = Path(config['projects_path'])
 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'])
 RULE_LOGS_PATH = Path(config['log_dir']) / 'rule_logs'
 RULE_LOGS_PATH.mkdir(parents=True, exist_ok=True)
 
-SAMPLES = get_samples(PEDIGREE_FPATH)
+SAMPLES = get_samples(PEDIGREE_FPATH)[:4]