diff --git a/workflows/simple_metaphlan2/SnakeFile b/workflows/simple_metaphlan2/SnakeFile index 8f939955b32bcf28fbd533248bcc31fe72b3f717..37c6ca8a62de4c9854617e1484675a55158f7be2 100644 --- a/workflows/simple_metaphlan2/SnakeFile +++ b/workflows/simple_metaphlan2/SnakeFile @@ -1,10 +1,10 @@ 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') diff --git a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile index dfd7278541c6e45454f5bb3cfa487759d7428d09..d7ba7747434ce714a545d159e27cc2527e0c8eb9 100644 --- a/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile +++ b/workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile @@ -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