1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
|
from pathlib import Path
# Untested:
# ancient
# subworkflows
# directory
OUTDIR = Path("outdir")
existing_file = Path("existing_file.txt")
rule all:
input:
OUTDIR / "output_existing",
OUTDIR / "output_temp",
OUTDIR / "output_protected",
OUTDIR / "output_other_rule_output_existing",
OUTDIR / "function_unpacking/output_function_unpacking",
rule input_Path:
input: Path("{sample}_file.txt")
output: OUTDIR / "output_{sample}"
log: OUTDIR / "log_{sample}"
shell:
"""
cat {input} > {output}
echo log {wildcards.sample} > {log}
"""
rule input_Path_output_temp:
input: existing_file
output: temp(OUTDIR / "output_temp")
log: OUTDIR / "log_temp"
shell:
"""
cat {input} > {output}
echo log temp > {log}
"""
rule input_Path_output_protected:
input: existing_file
output: protected(OUTDIR / "output_protected")
log: OUTDIR / "log_protected"
shell:
"""
cat {input} > {output}
echo log protected > {log}
"""
rule input_other_rule_output:
input: rules.input_Path.output
output: OUTDIR / "output_other_rule_output_{sample}"
log: OUTDIR / "log_other_rule_output_{sample}"
shell:
"""
cat {input} > {output}
echo log protected > {log}
"""
def myfunc1():
return [existing_file]
def myfunc2():
return {'existing_file2': existing_file}
rule input_function_unpacking:
input:
*myfunc1(),
**myfunc2(),
output: OUTDIR / "function_unpacking/output_function_unpacking"
log: OUTDIR / "log_function_unpacking"
shell:
"""
echo {input[0]} > {output}
echo {input.existing_file2} >> {output}
echo log function unpacking > {log}
"""
|
