User configurable hardware resources

Merge request

Please fill in the checklist below and comment as needed.

• Was code modified? Briefly describe. See below
• Was documentation modified? Briefly describe.
• Is this a bug-fix? Briefly describe. Yes. See below
• Is this a feature addition? Briefly describe. Yes. See below
• Did you modify QuaC-Watch config file? If so, did you modify multiqc template configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No
• Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why?
• Updated Changelog.md file with change logs in recommended format?

Anything else reviewer should know?

• Previously hardcoded hardware resources for snakemake rules can now be supplied via configs/workflow.yaml (closes #48 (closed))
• Modified multiqc conda env config to use explicit dependencies to get around installation issues (closes #47 (closed))

workflow/rules/common.smk

 import re
-import sys
-import json
 from snakemake.logging import logger
 
+
 def get_samples(ped_fpath):
     """
     Parse pedigree file and return sample names
@@ -98,12 +97,6 @@ def aggregate_rename_configs(rename_config_files, outfile):
 
     return None
 
-# def get_java_mem(cluster_config_file):
-#     print ('hey')
-#     # cluster_config_arg = sys.argv.index("--cluster-config")
-#     # cluster_config_file = sys.argv[cluster_config_arg + 1]
-#     cluster_config = json.load(open(cluster_config_file))
-#     return cluster_config.get("qualimap_bamqc", {}).get("mem-per-cpu", 24)
     
 ##########################   Configs from CLI  ##########################
 OUT_DIR = Path(config["out_dir"])
@@ -116,10 +109,6 @@ EXOME_MODE = config["exome"]
 RULE_LOGS_PATH = Path(config["log_dir"]) / "rule_logs"
 RULE_LOGS_PATH.mkdir(parents=True, exist_ok=True)
 
-
-# JAVA_MEM = get_java_mem(config["cluster_config"])
-# print(JAVA_MEM)
-
 SAMPLES = get_samples(PEDIGREE_FPATH)
 MULTIQC_CONFIG_FILE = OUT_DIR / "project_level_qc" / "multiqc" / "configs" / f"tmp_multiqc_config-{config['unique_id']}.yaml"