Very similar to Coupling inputs and outputs without shared wildcards, I have assembled a user-specified list of inputs and outputs that are paired:
inputs = ["/path/to/input1", "/path/to/input2"]
outputs = ["/path/to/output1", "/path/to/output2"]
In other words, I have a rule which should process input1 and generate output1, and in parallel the same rule may also process input2 and generate output2. I can try the recommended answer from the linked question, which looks like this, except I have used absolute paths, and remove the ".txt" suffix from the rules:
numbers = ['/tmp/1.txt', '/tmp/2.txt', '/tmp/3.txt', '/tmp/4.txt']
letters = ['/tmp/A.txt', '/tmp/B.txt', '/tmp/C.txt', '/tmp/D.txt']
ln = dict(zip(numbers, letters))
rule all:
input:
expand('{number}', number= numbers),
rule out:
input:
letter= lambda wc: ln[wc.number],
output:
'{number}'
shell:
"""
echo {input.letter} > {output}
"""
I have tried touching the inputs /tmp/A.txt, etc., however no matter how I try to arrange it, I get either key exceptions or missing input exceptions. However, if I use relative instead of absolute paths, I can get it to work. Is there any way to get it to work using all absolute paths?
The error occurs because the '{number}' wildcard is too broad. It can match any string, leading to unexpected behavior.
...
Error:
KeyError: '/tmp/A.txt' ## Notice here.
Wildcards:
number=/tmp/A.txt
...
To fix this, you can use wildcard_constraints to limit the scope of the number wildcard:
numbers = ['/tmp/1.txt', '/tmp/2.txt', '/tmp/3.txt', '/tmp/4.txt']
letters = ['/tmp/A.txt', '/tmp/B.txt', '/tmp/C.txt', '/tmp/D.txt']
ln = dict(zip(numbers, letters))
wildcard_constraints:
number="|".join(map(re.escape, numbers))
rule all:
input:
expand('{number}', number=numbers)
rule out:
input:
letter=lambda wc: ln[wc.number]
output:
'{number}'
shell:
"""
echo {input.letter} > {output}
"""
You can try below code to get a clearer error:
numbers = ['/tmp/1.txt', '/tmp/2.txt', '/tmp/3.txt', '/tmp/4.txt']
letters = ['/tmp/A.txt', '/tmp/B.txt', '/tmp/C.txt', '/tmp/D.txt']
ln = dict(zip(numbers, letters))
ln["/tmp/A.txt"] = "/tmp/1.txt"
rule all:
input:
expand('{number}', number= numbers),
def get_input(wc):
print(wc)
return ln[f"{wc.number}"]
rule outtes:
input:
letter= get_input,
output:
'{number}'
shell:
"""
echo {input.letter} > {output}
"""