defines log dir via cli

configs/cluster_config.json

@@ -4,7 +4,7 @@
         "partition": "express",
         "cpus-per-task": "{threads}",
         "mem": "8G",
-        "output": "{LOGS_PATH}/rule_logs/{rule}-%j.log"
+        "output": "{RULE_LOGS_PATH}/{rule}-%j.log"
     },
     "mosdepth": {
         "partition": "short",

configs/workflow.yaml

@@ -11,4 +11,3 @@ 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"
-logs_path: "logs/"

src/run_pipeline.py

@@ -62,7 +62,7 @@ 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}",
+        f"--config modules='{args.modules}' project_name={args.project_name} ped={args.pedigree} out_dir={args.outdir} log_dir={args.log_dir}",
         f"--restart-times {args.rerun_failed}",
         "--use-conda",
         f"--profile '{snakemake_profile_dir}'",
@@ -205,6 +205,14 @@ if __name__ == "__main__":
         metavar="",
     )
 
+    LOGS_DIR_DEFAULT = f"{QUAC_OUTDIR_DEFAULT}/../logs"
+    WRAPPER.add_argument(
+        "--log_dir",
+        help="Directory path where logs (both workflow and wrapper) will be stored",
+        default=LOGS_DIR_DEFAULT,
+        type=lambda x: is_valid_file(PARSER, x),
+        metavar="",
+    )
     WRAPPER.add_argument(
         "-e",
         "--extra_args",

workflow/rules/common.smk

@@ -62,7 +62,7 @@ PEDIGREE_FPATH = config['ped']
 
 #### configs from configfile ####
 PROJECTS_PATH = Path(config['projects_path'])
-LOGS_PATH = Path(config['logs_path'])
-LOGS_PATH.mkdir(parents=True, exist_ok=True)
+RULE_LOGS_PATH = Path(config['log_dir']) / 'rule_logs'
+RULE_LOGS_PATH.mkdir(parents=True, exist_ok=True)
 
 SAMPLES = get_samples(PEDIGREE_FPATH)