Reserved name in Snakemake?
Question:
I use Snakemake version 7.12.1 and I get the following error while trying to execute a pipeline:
AttributeError: invalid name for input, output, wildcard, params or
log: pop is reserved for internal use
I normally use the word pop as the wildcard for population with no issue. After the raised error, I made it changed to another word and it looks like the error is gone. Would someone confirm that pop is now a reserved name or there is another explanation for? I checked the snakemake manual and there is no any related notification.
Answers:
Would someone confirm that pop is now a reserved name or there is another explanation for?
Yes, pop is reserved because internally some processes use .pop method to remove items from the directives.
Internally, the directives (input/output/etc) are stored as a Namedlist which inherits methods from the list. So almost all the methods defined for list (and Namedlist) will trigger this error, e.g. remove, reverse. There are two hard-coded whitelisted exceptions: index and sort.
This change has been added a couple of years ago, so you must have been running a much older snakemake version.
Here’s a small Snakefile for testing:
rule all:
input: 'test.txt'
rule test:
output:
# this will err
pop = 'test.txt'
shell: 'echo {output}'
I use Snakemake version 7.12.1 and I get the following error while trying to execute a pipeline:
AttributeError: invalid name for input, output, wildcard, params or
log: pop is reserved for internal use
I normally use the word pop as the wildcard for population with no issue. After the raised error, I made it changed to another word and it looks like the error is gone. Would someone confirm that pop is now a reserved name or there is another explanation for? I checked the snakemake manual and there is no any related notification.
Would someone confirm that pop is now a reserved name or there is another explanation for?
Yes, pop is reserved because internally some processes use .pop method to remove items from the directives.
Internally, the directives (input/output/etc) are stored as a Namedlist which inherits methods from the list. So almost all the methods defined for list (and Namedlist) will trigger this error, e.g. remove, reverse. There are two hard-coded whitelisted exceptions: index and sort.
This change has been added a couple of years ago, so you must have been running a much older snakemake version.
Here’s a small Snakefile for testing:
rule all:
input: 'test.txt'
rule test:
output:
# this will err
pop = 'test.txt'
shell: 'echo {output}'