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Metagenomics
snakemake
Commits
34ac04e2
Commit
34ac04e2
authored
May 13, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
add possibility to change ref path to rules in config files
parent
8bb596da
Changes
2
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workflows/simple_metaphlan2/SnakeFile
View file @
34ac04e2
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')
...
...
workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
View file @
34ac04e2
...
...
@@ -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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