Snakemake workflow, ChildIOException or MissingInputException

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

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}"