Commit 52c704d8 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

fix Snakefile names

parent 9b5fbe32
......@@ -19,7 +19,7 @@ __metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
ext=__metaphlan2_input_type + ".gz")
__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
sample="{sample}")
include: "SnakeFile"
include: "Snakefile"
rule all:
input:
......
......@@ -17,7 +17,7 @@ __metaphlan2_heatmap_output_file_name = config['metaphlan2_heatmap'].get('output
__metaphlan2_heatmap_input = __input
__metaphlan2_heatmap_output = "{dir}/{file_name}".format(dir=__metaphlan2_heatmap_output_dir,
file_name=__metaphlan2_heatmap_output_file_name)
include: "SnakeFile"
include: "Snakefile"
rule all:
input:
......
......@@ -21,7 +21,7 @@ __metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__input_dir,
sample=config['samples'])
__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
file_name=__metaphlan2_merge_output_file_name)
include: "SnakeFile"
include: "Snakefile"
rule all:
input:
......
configfile: "config.yaml"
# ==== Rule paths ====
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/SnakeFile")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/Snakefile")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/Snakefile")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/Snakefile")
__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')
......@@ -39,7 +39,7 @@ include: __metaphlan2_heatmap_rules
# ---- Graphlan Dendogram
__graphlan_from_metaphlan2_output_dir = __main_output_dir + "/graphlan"
__graphlan_from_metaphlan2_output_file_name = config['graphlan_from_metaphlan2'].get('output_name',"dendogram.png")
__graphlan_from_metaphlan2_output_file_name = config.get("graphlan_from_metaphlan2", {}).get('output_name',"dendogram.png")
__graphlan_from_metaphlan2_input = __metaphlan2_merge_output
__graphlan_from_metaphlan2_output = "{dir}/{file_name}".format(dir=__graphlan_from_metaphlan2_output_dir,
file_name=__graphlan_from_metaphlan2_output_file_name)
......
......@@ -8,9 +8,9 @@ This subworkflow need to be called to be used by specifying:
"""
# ==== Rule paths ====
__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/SnakeFile")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/SnakeFile")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/SnakeFile")
__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/Snakefile")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/Snakefile")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/Snakefile")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
......
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