Snakemake workflow, ChildIOException or MissingInputException - workflow

Question

I am trying to add a file renaming step in my current workflow to make it easier on some of the other users. What I want to do is take the contigs.fasta file from a spades assembly directory and rename it to include the sample name. (i.e foo_de_novo/contigs.fasta to foo_de_novo/foo.fasta)
here is my code... well currently.
configfile: "config.yaml"
import os
def is_file_empty(file_path):
""" Check if file is empty by confirming if its size is 0 bytes"""
# Check if singleton file exist and it is empty from bbrepair output
return os.path.exists(file_path) and os.stat(file_path).st_size == 0
rule all:
input:
expand("{sample}_de_novo/{sample}.fasta", sample = config["names"]),
rule fastp:
input:
r1 = lambda wildcards: config["sample_reads_r1"][wildcards.sample],
r2 = lambda wildcards: config["sample_reads_r2"][wildcards.sample]
output:
r1 = temp("clean/{sample}_r1.trim.fastq.gz"),
r2 = temp("clean/{sample}_r2.trim.fastq.gz")
shell:
"fastp --in1 {input.r1} --in2 {input.r2} --out1 {output.r1} --out2 {output.r2} --trim_front1 20 --trim_front2 20"
rule bbrepair:
input:
r1 = "clean/{sample}_r1.trim.fastq.gz",
r2 = "clean/{sample}_r2.trim.fastq.gz"
output:
r1 = temp("clean/{sample}_r1.fixed.fastq"),
r2 = temp("clean/{sample}_r2.fixed.fastq"),
singles = temp("clean/{sample}.singletons.fastq")
shell:
"repair.sh -Xmx10g in1={input.r1} in2={input.r2} out1={output.r1} out2={output.r2} outs={output.singles}"
rule spades:
input:
r1 = "clean/{sample}_r1.fixed.fastq",
r2 = "clean/{sample}_r2.fixed.fastq",
s = "clean/{sample}.singletons.fastq"
output:
directory("{sample}_de_novo")
run:
isempty = is_file_empty("clean/{sample}.singletons.fastq")
if isempty == "False":
shell("spades.py --careful --phred-offset 33 -1 {input.r1} -2 {input.r2} -s {input.singletons} -o {output}")
else:
shell("spades.py --careful --phred-offset 33 -1 {input.r1} -2 {input.r2} -o {output}")
rule rename_spades:
input:
"{sample}_de_novo/contigs.fasta"
output:
"{sample}_de_novo/{sample}.fasta"
shell:
"cp {input} {output}"
When I have it written like this I get the MissingInputError and when I change it to this.
rule rename_spades:
input:
"{sample}_de_novo"
output:
"{sample}_de_novo/{sample}.fasta"
shell:
"cp {input} {output}"
I get the ChildIOException
I feel I understand why snakemake is unhappy with both versions. The first one is becasue I don't explicitly output the "{sample}_de_novo/contigs.fasta" file. Its just one of several files spades outputs. And the other error is because it doesn't like how I am asking it to look into the directory. I however am at a loss on how to fix this.
Is there a way to ask snakmake to look into a directory for a file and then perform the task requested?
Thank you,
Sean
EDIT File Structure of Spades output
Sample_de_novo
|-corrected/
|-K21/
|-K33/
|-K55/
|-K77/
|-misc/
|-mismatch_corrector/
|-tmp/
|-assembly_graph.fastg
|-assembly_graph_with_scaffolds.gfa
|-before_rr.fasta
|-contigs.fasta
|-contigs.paths
|-dataset.info
|-input_dataset.ymal
|-params.txt
|-scaffolds.fasta
|-scaffolds.paths
|spades.log

Answer 1

Make {sample}_de_novo/contigs.fasta to be the output of spades and parse its path to get the directory that will be the argument to spades -o. Snakemake won't mind if there are other files created in addition to contigs.fasta. This should run --dry-run mode:
rule all:
input:
expand('{sample}_de_novo/{sample}.fasta', sample=['A', 'B']),
rule spades:
output:
fasta='{sample}_de_novo/contigs.fasta',
run:
outdir=os.path.dirname(output.fasta)
shell(f'spades ... -o {outdir}')
rule rename:
input:
fasta='{sample}_de_novo/contigs.fasta',
output:
fasta='{sample}_de_novo/{sample}.fasta',
shell:
r"""
mv {input.fasta} {output.fasta}
"""

Answer 2

Nope, spoke too soon. It didn't name the output directory correctly, so I moved it to the params and, now, finailly is working the way I wanted.
rule spades:
input:
r1 = "clean/{sample}_r1.fixed.fastq",
r2 = "clean/{sample}_r2.fixed.fastq",
s = "clean/{sample}.singletons.fastq"
output:
"{sample}_de_novo/contigs.fasta"
params:
outdir = directory("{sample}_de_novo/")
run:
isempty = is_file_empty("clean/{sample}.singletons.fastq")
if isempty == "False":
shell("spades.py --isolate --phred-offset 33 -1 {input.r1} -2 {input.r2} -s {input.singletons} -o {params.outdir}")
else:
shell("spades.py --isolate --phred-offset 33 -1 {input.r1} -2 {input.r2} -o {params.outdir}")
rule rename_spades:
input:
"{sample}_de_novo/contigs.fasta"
output:
"{sample}_de_novo/{sample}.fasta"
shell:
"cp {input} {output}"