Using * to glob within an input file, or using multiple wildcards in input, then using only one wildcard for output? - snakemake

Question

Is there a way to write a rule so that I don't need to use the wildcards for all inputs/outputs or can I use a "*" to glob rather than using wildcards?? I want to symlink a file that is autocreated in subfolders, to the main directory.
This is the error I get when trying to run the Snakemake:
WildcardError in line 42 of snakemake_guppy_basecall/Snakefile:
Wildcards in input files cannot be determined from output files:
'failpass'
import glob
configfile: "config.yaml"
inputdirectory=config["directory"]
SAMPLES, = glob_wildcards(inputdirectory+"/{sample}.fast5", followlinks=True)
print(SAMPLES)
wildcard_constraints:
sample="\w+\d+_\w+_\w+\d+_.+_\d"
##### target rules #####
rule all:
input:
#expand('basecall/{sample}/sequencing_summary.txt', sample=SAMPLES),
"qc/multiqc.html"
rule make_indvidual_samplefiles:
input:
inputdirectory+"/{sample}.fast5",
output:
"lists/{sample}.txt",
shell:
"basename {input} > {output}"
rule guppy_basecall_persample:
input:
directory=directory(inputdirectory),
samplelist="lists/{sample}.txt",
output:
summary="basecall/{sample}/sequencing_summary.txt",
directory=directory("basecall/{sample}/"),
params:
config["basealgo"]
shell:
"guppy_basecaller -i {input.directory} --input_file_list {input.samplelist} -s {output.directory} -c {params} --compress_fastq -x \"auto\" --gpu_runners_per_device 3 --num_callers 2 --chunks_per_runner 200"
rule guppy_linkfastq:
input:
#glob_wildcards("basecall/{sample}/*/*.fastq.gz"),
"basecall/{sample}/{failpass}/{runid}.fastq.gz",
output:
"basecall/{sample}.fastq.gz",
shell:
"ln -s {input} {output}"
rule fastqc_pretrim:
input:
#"basecall/{sample}/{failpass}/{runid}.fastq.gz",
"basecall/{sample}.fastq.gz"
output:
html="qc/fastqc_pretrim/{sample}.html",
zip="qc/fastqc_pretrim/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
params: ""
log:
"logs/fastqc_pretrim/{sample}.log"
threads: 1
wrapper:
"v0.75.0/bio/fastqc"
rule multiqc:
input:
#expand("basecall/{sample}.fastq.gz", sample=SAMPLES)
expand("qc/fastqc_pretrim/{sample}_fastqc.zip", sample=SAMPLES)
output:
"qc/multiqc.html"
params:
"" # Optional: extra parameters for multiqc.
log:
"logs/multiqc.log"
wrapper:
"0.77.0/bio/multiqc"
I am trying to create a pipeline that does: Get Nanopore f5 sequence files -> run guppy basecaller GPU mode -> use resulting fastq files to run FASTQC -> run multiQC for everything