Hi there,

I am using snakemake to compile a pipeline and encounter an issue as follows:

The error reported is:

RuleException in line 284 of pipeline_1.snakemake: Wildcards in input, params, log or benchmark file of rule fastx_collapser cannot be determined from output files: 'PIPELINE_NAME'

The scripts in snakemake file is:

PIPELINE_NAME = "pipeline_1"

FOLDER = "/data/analysis/"

    rule test1:

        input:
            "{FOLDER}/raw/{smp}.txt"
        output:
            "{FOLDER}/processed/{smp}.result.txt"
        log:
            out="{FOLDER}/{PIPELINE_NAME}/logs/{smp}.log.stdout",
            err="{FOLDER}/{PIPELINE_NAME}/logs/{smp}.log.stderr"
        shell: """
               program -i {input} -o {output} 2> {log.err} 1> {log.out}
               """

BTW, when the log function is not used, there is no problem. Therefore, I am just thinking about something wrong with the log file function.

Would you like to help me out about this problem?

Thank you very much,

Regards,

Tom