Understanding and overcoming AmbiguousRuleException in snakemake

Question

I have a complicated workflow which I progressively extended. The last extension resulted in an AmbiguousRuleException. I tried to reproduce the critical structure of the workflow in the following example:

NUMBERS = ["1", "2"]
LETTERS = ["a", "b", "c"]
WORDS = ["foo", "bar", "baz"]
CHOICES = ["yes", "no"]


rule all:
    input:
        # (1)
        expand("results/allthings/{word}_{choice}.md5sum", word=WORDS, choice=CHOICES)
        #expand("results/allthings/{word}_{choice}.md5sum", word=WORDS + ["all"], choice=CHOICES)

rule make_things:
    output:
        "results/{letter}_{number}/{word}_{choice}.txt"
    shell:
        """
        echo "{wildcards.letter}_{wildcards.number}_{wildcards.word}_{wildcards.choice}" > {output}
        """

rule gather_things:
    input:
        expand("results/{letter}_{number}/{{word}}_{{choice}}.txt", letter=LETTERS, number=NUMBERS)
    output:
        "results/allthings/{word}_{choice}.txt"
    shell:
        """
        cat {input} > {output}
        """

# (2)
#rule join_all_words:
#    input:
#        expand("results/allthings/{word}_{{choice}}.txt", word=WORDS)
#    output:
#        "results/allthings/all_{choice}.txt"
#    shell:
#        """
#        cat {input} > {output}
#        """
# (3)
#def source_data(wildcards):
#    if wildcards.word == "all":
#        return rules.join_all_words.output
#    else:
#        return rules.gather_things.output

rule compute_md5:
    input:
        # (4)
        rules.gather_things.output,
        #source_data
    output:
        "results/allthings/{word}_{choice}.md5sum"
    shell:
        """
        md5sum {input} > {output}
        """

The above state is functional. Switching (1) and (4) and uncommenting (2) and (3) correspond to the extension I'm trying to make, and results in the following failure:

AmbiguousRuleException:
Rules gather_things and join_all_words are ambiguous for the file results/allthings/all_yes.txt.
Expected input files:
    gather_things: results/a_1/all_yes.txt results/a_2/all_yes.txt results/b_1/all_yes.txt results/b_2/all_yes.txt results/c_1/all_yes.txt results/c_2/all_yes.txt
    join_all_words: results/allthings/foo_yes.txt results/allthings/bar_yes.txt results/allthings/baz_yes.txt

It seems that snakemake thinks that results/allthings/all_yes.txt can be generated by gather_things.

Why?

How can I avoid that?

Note: The goal of modifications (3) and (4) is to have the compute_md5 work on both the direct output of gather_things (for foo, bar and baz) and the joined output of the three (all), keeping input defined in terms of other rule's output as much as possible (which makes changes easier than when file names are explicitly used).

Understanding and overcoming AmbiguousRuleException in snakemake

1 Answers