title: snakemake wildcard in input files
body: <p>I am very new to snakemake and I am trying to create a merged.fastq for each sample. Following is my Snakefile.</p>
  <pre><code>configfile: &quot;config.yaml&quot;
  print(config['samples'])
  print(config['ss_files'])
  print(config['pass_files'])
  
  rule all:
      input:
          expand(&quot;{sample}/data/genome_assembly/medaka/medaka.fasta&quot;, sample=config[&quot;samples&quot;]),
          expand(&quot;{pass_file}&quot;, pass_file=config[&quot;pass_files&quot;]),
          expand(&quot;{ss_file}&quot;, ss_file=config[&quot;ss_files&quot;]) 
  
  rule merge_fastq:
      input: 
          directory(&quot;{pass_file}&quot;)
      output: 
          &quot;{sample}/data/merged.fastq.gz&quot;
      wildcard_constraints:
          id=&quot;*.fastq.gz&quot;
      shell:
          &quot;cat {input}/{id} &gt; {output}&quot;   
  </code></pre>
  <p>where, 'samples' is a list of sample names,<br />
  'pass_files' is a list of directory path to fastq_pass folder which contains small fastq files</p>
  <p>I am trying to merge small fastq files to a large merged.fastq for each sample.</p>
  <p>I am getting the following,</p>
  <blockquote>
  <p>Wildcards in input files cannot be determined from output files:
  'pass_file'</p>
  </blockquote>
  <p>as the error.</p>