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Metagenomics
snakemake
Commits
52c704d8
Commit
52c704d8
authored
May 13, 2019
by
Kenzo-Hugo Hillion
♻
Browse files
fix Snakefile names
parent
9b5fbe32
Changes
12
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tools/graphlan/export2graphlan/Snake
F
ile
→
tools/graphlan/export2graphlan/Snake
f
ile
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52c704d8
File moved
tools/graphlan/graphlan/Snake
F
ile
→
tools/graphlan/graphlan/Snake
f
ile
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52c704d8
File moved
tools/graphlan/graphlan_annotate/Snake
F
ile
→
tools/graphlan/graphlan_annotate/Snake
f
ile
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52c704d8
File moved
tools/metaphlan2/metaphlan2/Snake
F
ile
→
tools/metaphlan2/metaphlan2/Snake
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ile
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52c704d8
File moved
tools/metaphlan2/metaphlan2/usage_example.rules
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52c704d8
...
...
@@ -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: "Snake
F
ile"
include: "Snake
f
ile"
rule all:
input:
...
...
tools/metaphlan2/metaphlan2_heatmap/Snake
F
ile
→
tools/metaphlan2/metaphlan2_heatmap/Snake
f
ile
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52c704d8
File moved
tools/metaphlan2/metaphlan2_heatmap/usage_example.rules
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...
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@@ -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: "Snake
F
ile"
include: "Snake
f
ile"
rule all:
input:
...
...
tools/metaphlan2/metaphlan2_merge/Snake
F
ile
→
tools/metaphlan2/metaphlan2_merge/Snake
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ile
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52c704d8
File moved
tools/metaphlan2/metaphlan2_merge/usage_example.rules
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52c704d8
...
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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: "Snake
F
ile"
include: "Snake
f
ile"
rule all:
input:
...
...
workflows/simple_metaphlan2/Snake
F
ile
→
workflows/simple_metaphlan2/Snake
f
ile
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52c704d8
configfile: "config.yaml"
# ==== Rule paths ====
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/Snake
F
ile")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/Snake
F
ile")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/Snake
F
ile")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/Snake
F
ile")
__metaphlan2_rules = config.get("rules", {}).get("metaphlan2", "../../tools/metaphlan2/metaphlan2/Snake
f
ile")
__metaphlan2_merge_rules = config.get("rules", {}).get("metaphlan2_merge", "../../tools/metaphlan2/metaphlan2_merge/Snake
f
ile")
__metaphlan2_heatmap_rules = config.get("rules", {}).get("metaphlan2_heatmap", "../../tools/metaphlan2/metaphlan2_heatmap/Snake
f
ile")
__graphlan_from_metaphlan2_rules = config.get("rules", {}).get("graphlan_from_metaphlan2", "../subworkflows/graphlan_from_metaphlan2/Snake
f
ile")
__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)
...
...
workflows/subwor
f
klows/README.md
→
workflows/subwork
f
lows/README.md
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52c704d8
File moved
workflows/subwor
f
klows/graphlan_from_metaphlan2/Snake
F
ile
→
workflows/subwork
f
lows/graphlan_from_metaphlan2/Snake
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ile
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52c704d8
...
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@@ -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/Snake
F
ile")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/Snake
F
ile")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/Snake
F
ile")
__export2graphlan_rules = config.get("rules", {}).get("export2graphlan", "../../tools/metaphlan2/metaphlan2/Snake
f
ile")
__graphlan_annotate_rules = config.get("rules", {}).get("graphlan_annotate", "../../tools/metaphlan2/metaphlan2_merge/Snake
f
ile")
__graphlan_rules = config.get("rules", {}).get("graphlan", "../../tools/metaphlan2/metaphlan2_heatmap/Snake
f
ile")
# ---- export2graphlan
__export2graphlan_input = __graphlan_from_metaphlan2_input
...
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