feat: add max_time_hr option for wall-time allocation

This commit introduces a new optional parameter, `max_time_hr`, in
the config file. Users can specify an integer value representing the
maximum wall-time allocation in hours. This feature is particularly
beneficial for the time-intensive rules `population_level_ibd` and
`sample_concordance_plink`, allowing users to manage resource limitations
on their clusters effectively.

src/cgr_gwas_qc/models/config/software_params.py

@@ -28,7 +28,6 @@ class SoftwareParams(BaseModel):
             pi_hat_threshold: 0.2
 
             autosomal_het_threshold: 0.1
-
     """
 
     strand: str = Field(

src/cgr_gwas_qc/models/config/workflow_params.py

@@ -1,4 +1,5 @@
 import time
+from typing import Optional
 
 from pydantic import BaseModel, Field
 
@@ -23,6 +24,7 @@ class WorkflowParams(BaseModel):
             lims_upload: true
             lims_output_dir: /DCEG/CGF/Laboratory/LIMS/drop-box-prod/gwas_primaryqc/
             case_control_gwas: false
+            max_time_hr:
             time_start:
     """
 
@@ -87,6 +89,12 @@ class WorkflowParams(BaseModel):
         False,
         description="A plink logistic regression gwas will be performed with case_control phenotype.",
     )
+
+    max_time_hr: Optional[int] = Field(
+        None,
+        description="Allocates the specified number of hours for the execution of the ``sample_concordance_plink`` and ``population_level_ibd`` rules.",
+    )
+
     time_start: str = Field(
         timestr,
         description="Date and time at which the workflow starts. This creates a unique id for the run.",

src/cgr_gwas_qc/workflow/sub_workflows/sample_qc.smk

@@ -2,8 +2,8 @@ from cgr_gwas_qc import load_config
 
 cfg = load_config()
 
-BIG_TIME = {1: 10, 2: 48, 3: 96}
-
+mtime = cfg.config.workflow_params.max_time_hr
+BIG_TIME = dict.fromkeys(range(1, 4), mtime) if mtime else {1: 10, 2: 48, 3: 96}
 
 use_contamination = (
     cfg.config.user_files.idat_pattern

src/cgr_gwas_qc/workflow/sub_workflows/subject_qc.smk

@@ -9,8 +9,8 @@ import math
 
 cfg = load_config()
 
-PLINK_BIG_MEM = {1: 1024 * 4, 2: 1024 * 64, 3: 1024 * 250}
-BIG_TIME = {1: 8, 2: 24, 3: 48}
+mtime = cfg.config.workflow_params.max_time_hr
+BIG_TIME = dict.fromkeys(range(1, 4), mtime) if mtime else {1: 8, 2: 24, 3: 48}
 
 
 localrules:
@@ -280,7 +280,7 @@ use rule genome from plink as population_level_ibd with:
     output:
         "subject_level/{population}/subjects_maf{maf}_ld{ld}_ibd.genome",
     resources:
-        mem_mb=lambda wildcards, attempt: PLINK_BIG_MEM[attempt],
+        mem_mb=lambda wildcards, attempt, input: max((attempt + 1) * input.size_mb, 1024),
         time_hr=lambda wildcards, attempt: BIG_TIME[attempt],