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Metagenomics
snakemake
Commits
9b5fbe32
Commit
9b5fbe32
authored
May 13, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
rename all as SnakeFile
parent
34ac04e2
Changes
11
Hide whitespace changes
Inline
Side-by-side
tools/graphlan/export2graphlan/
export2graphlan.ru
le
s
→
tools/graphlan/export2graphlan/
SnakeFi
le
View file @
9b5fbe32
File moved
tools/graphlan/graphlan/
graphlan.ru
le
s
→
tools/graphlan/graphlan/
SnakeFi
le
View file @
9b5fbe32
File moved
tools/graphlan/graphlan_annotate/
graphlan_annotate.ru
le
s
→
tools/graphlan/graphlan_annotate/
SnakeFi
le
View file @
9b5fbe32
File moved
tools/metaphlan2/metaphlan2/
metaphlan2.ru
le
s
→
tools/metaphlan2/metaphlan2/
SnakeFi
le
View file @
9b5fbe32
File moved
tools/metaphlan2/metaphlan2/usage_example.rules
View file @
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: "
metaphlan2.ru
le
s
"
include: "
SnakeFi
le"
rule all:
input:
...
...
tools/metaphlan2/metaphlan2_heatmap/
metaphlan2_heatmap.ru
le
s
→
tools/metaphlan2/metaphlan2_heatmap/
SnakeFi
le
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9b5fbe32
File moved
tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
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9b5fbe32
...
...
@@ -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: "
metaphlan2_heatmap.ru
le
s
"
include: "
SnakeFi
le"
rule all:
input:
...
...
tools/metaphlan2/metaphlan2_merge/
metaphlan2_merge.ru
le
s
→
tools/metaphlan2/metaphlan2_merge/
SnakeFi
le
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9b5fbe32
File moved
tools/metaphlan2/metaphlan2_merge/usage_example.rules
View file @
9b5fbe32
...
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@@ -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: "
metaphlan2_merge.ru
le
s
"
include: "
SnakeFi
le"
rule all:
input:
...
...
workflows/simple_metaphlan2/SnakeFile
View file @
9b5fbe32
configfile: "config.yaml"
# ==== Rule paths ====
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/
metaphlan2.ru
le
s
")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/
metaphlan2_merge.ru
le
s
")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/
metaphlan2_heatmap.ru
le
s
")
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/
SnakeFi
le")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/
SnakeFi
le")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/
SnakeFi
le")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/SnakeFile")
__input_dir = config['input_dir']
...
...
workflows/subworfklows/graphlan_from_metaphlan2/SnakeFile
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9b5fbe32
...
...
@@ -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/
metaphlan2.ru
le
s
")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/
metaphlan2_merge.ru
le
s
")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/
metaphlan2_heatmap.ru
le
s
")
__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/
SnakeFi
le")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/
SnakeFi
le")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/
SnakeFi
le")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
...
...
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