Snakemake not recognizing multiple files as input

Question

I'm having some trouble running snakemake. I want to perform quality control of some RNA-Seq bulk samples using FastQC. I've written the code in a way that all files following the pattern {sample}_{replicate}.fastq.gz should be used as input, where {sample} is the sample id (i.e. SRR6974023) and {replicate} is 1 or 2. My little scripts follows:

configfile: "config.yaml"

rule all:
  input:
    expand("raw_qc/{sample}_{replicate}_fastqc.{extension}", sample=config["samples"], replicate=[1, 2], extension=["zip", "html"])
    

rule fastqc:
  input:
    rawread=expand("raw_data/{sample}_{replicate}.fastq.gz", sample=config["samples"], replicate=[1, 2])
  
  output:
    compress=expand("raw_qc/{sample}_{replicate}_fastqc.zip", sample=config["samples"], replicate=[1, 2]),
    net=expand("raw_qc/{sample}_{replicate}_fastqc.html", sample=config["samples"], replicate=[1, 2])
  
  threads: 
    8
  
  params:
    path="raw_qc/"
  
  shell:
    "fastqc -t {threads} {input.rawread} -o {params.path}" 

Just is case, the config.yaml is:

samples:
  SRR6974023
  SRR6974024

The raw_data directory with my files look like this:

SRR6974023_1.fastq.gz  SRR6974023_2.fastq.gz  SRR6974024_1.fastq.gz  SRR6974024_2.fastq.gz

Finally, when I run the script, I always see the same error:

Building DAG of jobs...
MissingInputException in line 8 of /home/user/path/Snakefile:
Missing input files for rule fastqc:
raw_data/SRR6974023 SRR6974024_2.fastq.gz
raw_data/SRR6974023 SRR6974024_1.fastq.gz

It see correctly only the last files, in this case SRR6974024_1.fastq.gz and SRR6974024_2.fastq.gz. Whatsoever, the other one it's only seen as SRR6974023. How can I solve this issue? I appreciate some help. Thank you all!

Answer 1

The yaml is not configured correctly. It should have - to turn each row into a list:

samples:
  - SRR6974023
  - SRR6974024