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Sometimes user expects that he is using already defined variable or rule section, but get error like: wildcard threads cannot be defined from input/output error. E.g. in:
rule:
threads: 4
params: extra = "--cores {threads}"
fails in snakemake, should be
...
params: extra = lambda wildcards, threads: f"--core {threads}"
Inspection: warn if user tries to use input/output/threads/etc when user is supposed to use lambda fun (it is general use-case for Inspection: wildcards in shell script can be used only with wildcards. prefix. #57), see {thread} related example in the beginning of this post. It is kind of hint for user, not just unresolved reference or user can fail to notice wildcard highlighting (depends on color scheme)
Sometimes user expects that he is using already defined variable or rule section, but get error like: wildcard
threads
cannot be defined from input/output error. E.g. in:fails in snakemake, should be
In this issue let's
wildcards.foo
same as in injection '{foo}' Highlight wildcard name afterwildcards.foo
same as in injection '{foo}' #227input/output/threads/etc
when user is supposed to use lambda fun (it is general use-case for Inspection: wildcards in shell script can be used only withwildcards.
prefix. #57), see{thread}
related example in the beginning of this post. It is kind of hint for user, not just unresolved reference or user can fail to notice wildcard highlighting (depends on color scheme)input
,output
,log
,message
and other required sections (check snakemake sources & runtime behaviour). In such cases snakemake shows runtime error Inpsection: warn if wildcards set is different in input, output, log, message and other required sections (check snakemake sources & runtime behaviour). #207{..}
(PR #184 determine wildcard names for rule #225)wildcards.
prefix. So it is hint for user, not just unresolved reference. Inspection: wildcards in shell script can be used only withwildcards.
prefix. #57The text was updated successfully, but these errors were encountered: