text: user16331: I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.
  Error: Building DAG of jobs...
  MissingRuleException:
  No rule to produce snakefile (if you use input functions make sure that they don't raise unexpected exceptions).
  
  Code:
  rule salmon_index:
          input:
                  R1="sequences/*R1.fastq.gz",
                  R2="sequences/*R2.fastq.gz"
          output:
                  Index="results/salmon_index"
          shell:
                  """
                  salmon index --threads 8 -t references/genome.fa.gz -i salmon_index
                  """
  
  
  user650: You're not using wildcards the way snakemake is equipped to work with them. See:
  
  FAQs such as https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory and https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do
  https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards
  
  
original_text: 16331: <p>I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.</p>
  <pre><code>Error: Building DAG of jobs...
  MissingRuleException:
  No rule to produce snakefile (if you use input functions make sure that they don't raise unexpected exceptions).
  </code></pre>
  <p>Code:</p>
  <pre><code>rule salmon_index:
          input:
                  R1=&quot;sequences/*R1.fastq.gz&quot;,
                  R2=&quot;sequences/*R2.fastq.gz&quot;
          output:
                  Index=&quot;results/salmon_index&quot;
          shell:
                  &quot;&quot;&quot;
                  salmon index --threads 8 -t references/genome.fa.gz -i salmon_index
                  &quot;&quot;&quot;
  </code></pre>
   650: <p>You're not using wildcards the way snakemake is equipped to work with them. See:</p>
  <ol>
  <li>FAQs such as <a href="https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory</a> and <a href="https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do</a></li>
  <li><a href="https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards</a></li>
  </ol>
  