Commit 34ac04e2 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add possibility to change ref path to rules in config files

parent 8bb596da
configfile: "config.yaml"
# ==== Rule paths ====
__metaphlan2_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
__metaphlan2_merge_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
__metaphlan2_heatmap_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
__graphlan_from_metaphlan2_rules = "../subworkflows/graphlan_from_metaphlan2/SnakeFile"
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
__input_dir = config['input_dir']
__main_output_dir = config.get('output_dir', 'output')
......
......@@ -8,9 +8,9 @@ This subworkflow need to be called to be used by specifying:
"""
# ==== Rule paths ====
__export2graphlan_rules = "../../tools/metaphlan2/metaphlan2/metaphlan2.rules"
__graphlan_annotate_rules = "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules"
__graphlan_rules = "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules"
__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/metaphlan2.rules")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/metaphlan2_heatmap.rules")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
......
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