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Explicit conda env

Closed Manavalan Gajapathy requested to merge explicit_conda_env into flexible_input_reqts
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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"
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