Snakemake MissingExceptionOutput

Question

[ohu20a]

Please, does not anyone know why this code is giving "MissingOutputException" in Snakemake even though the dry-run worked fine.

rule all:
    input:
       expand(os.path.join(config["input_dir"], "input/{sample}.txt"), sample = ["A","B"]),

rule create_file:
    output:
        os.path.join(config["input_dir"], "input/{sample}.txt"),
    log:
        os.path.join(config["log_dir"], "input/{sample}.log"),
    shell:
        'echo {wildcards.sample} > {output}'

Error:

MissingOutputException in line 8 of  /yates_CNV_after_merging/rules/cnv.smk

[cpad0112]

Error refers cnv.smk. Please post the contents of cnv.smk.

[dariober]

I cannot reproduce your issue. I copied your two rules to file Snakefile and executed it with snakemake -j 1 -C log_dir='.' input_dir='.' and it completed without errors. Maybe there is something you are not showing?