I’m writing a Snakemake pipeline to run some simulations. The key points are that:
(1) I run simulations across a space of values of parameters A, B & C and in n replicates,
(2) I plot the results averaged across the replicates for each parameter combination,
(3) I want to combine the plots so that, for each combination of B & C, I produce a plot with panels for different values of A.

I’m getting a MissingInputException error associated with step 3.

A minimal version of my Snakefile looks as follows:

A_lst = [0.0, 0.1, 0.01]
B_lst = [0.0, 0.1, 0.01]
C_lst = [0.0, 0.1, 0.01]

seeds = [2,22,42]

rule all:
    input:
        expand("sims/A~{A}/B~{B}/C~{C}/{seed}.out", A=A_lst, B=B_lst, C=C_lst, seed=seeds),
        expand("sims/A~{A}/B~{B}/C~{C}/plot.png", A=A_lst, B=B_lst, C=C_lst),
        expand("plots/combined_B{B}_C{C}.png", B=B_lst, C=C_lst)

rule simulate:
    output:
        "sims/A~{A}/B~{B}/C~{C}/{seed}.out"
    shell:
        "simulator {wildcards.A} {wildcards.B} {wildcards.C} {wildcards.rep}"

rule plot:
    input:
        expand("sims/A~{{A}}/B~{{B}}/C~{{C}}/{seed}.out", seed=seeds)
    output:
        "sims/A~{A}/B~{B}/C~{C}/plot.png"
    shell:
        "scripts/plot.py"


rule combine_plots:
    input:
        expand("output/A~{A}/B~{{B}}/C~{{C}}/plot.png",
        A=A_lst)
    output:
        "plots/combined_B{B}_C{C}.png"
    script:
        "scripts/combine_plots.py"

This gives the following error:

# executing snakemake -n --cores 1 --conda-frontend conda --use-conda
Building DAG of jobs...
MissingInputException in rule all in file /data/username/project/Snakefile, line 67:
Missing input files for rule all:
    affected files:
        plots/combined_B0.0_C0.0.png

This surprises me. I thought that the logic would be here as follows:
(1) ask for all possible parameter combination of plots/combined_B{B}_C{C}.png
(2) expand on A while matching the values of B & C from the output
…

The previous two rules work. However, everything to generate plots/combined_B0.0_C0.0.png also seems to be there? I would appreciate some explanation and a suggestion of how to fix it!

Thanks in advance!