Snakemake with R Problem cannot find output files

I'm trying to make bioinformatics work "easier" for myself with Snakemake 😊, but my first attempts unfortunately caused me problems. Unfortunately, I could not find a solution on the internet on all common platforms that would have eliminated the problem. Therefore, I thought that our "swarm intelligence/swarm experience" might be more helpful in troubleshooting 😊.

I would like to automate my R analyses with Snakemake:

My Snakefile:

rule hello:
    output:  
        filtered_file = "output.csv"
    input:
        script='scripts/test.r',
        annotations_file="cars.csv"
    shell:
       "Rscript {input.script} \
        --annotations_file {input.annotations_file} \
        --filtered_file {output.filtered_file}"

My Rscript

library(dplyr)
annot_data=read.csv2(snakemake@input[["annotations_file"]],header=TRUE)
filtered = annot_data %>% filter(speed > 7))
write.csv2(filtered,snakemake@output[["filtered_file"]])

When I perform a "dry run", I always get the error message that the "output files" cannot be found (see below). The second problem, when I run my scripts an Error occurs without any explanations. Do you have any idea what I'm doing wrong or how I can tame the "snakemake(r)" 😊?

Any help appreciated
Many thanks in advance for your help

Best regards

Pavlo

I have already tried various solutions ["from the internet"] (https://stackoverflow.com/questions/68620638/how-to-execute-r-inside-snakemake) or e.g. [modification of Snakefile] (https://github.com/fritzbayer/snakemake-with-R) or this - unfortunately without success.

This is intended and normal behaviour for snakemake and one of the reasons to actually use the software.

Snakemake is telling you the reason, why it will execute the rule hello: The purpose of the rule is to provide the output file output.csv and the file is missing. So snakemake would like to run this specific rule in order to produce the output file.

Thank you very much @euronion for your answer, unfortunately the problem was elsewhere. When I started snakemake directly and not in dry-run mode, the same error was displayed in the log file without further explanation. Later I found out that it was because the *.r extension in the name of my rscript was lower case, while in examples from the internet *.R is capitalised. Once I changed the extension in the name of my rskript to upper case, everything worked 😊. Apparently the snakefile does not see/accept the lower case extension in the name of a script test. You have to know that first 😊 and figure it out. So, the first hurdle in the "Snakemake world" is cleared and that's a good feeling.

Best regards
Pavlo