text: user14547: I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error "Multiple run or shell keywords in rule run_fastqc".
  Snakefile:
  rule run_fastqc:
      input:
          "/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz"
      output:
          "./[out path]/well01_S001_L001_R1_001.fastqc.html",
          "./[out path]/well01_S001_L001_R1_001.fastqc.zip"
      wrapper:
          "0.79.0/bio/fastqc"
      shell:
          "fastqc {input} --outdir=./[out path]/"
  
  I've also tried:
  ...
      shell:
          "fastqc {input} -o ./[out path]/"
  ...
      shell:
          "fastqc -o ./[out path]/ {input}"
  ...
      shell:
          "fastqc {input}"
          "fastqc -o ./[out path]/"
  ...
      shell:
          "fastqc {input} > -o ./[out path]/"
  
  Code:
  snakemake --cores 1 well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip
  
  Output:
  SyntaxError in line 9 of /[path to Snakefile]/Snakefile:
  Multiple run or shell keywords in rule run_fastqc. (Snakefile, line 9)
  
  When I run fastqc alone (not in snakemake), it works and I get the two output files. How can I get snakemake to work?
  Thank you for your time and help!
  
  user650: From a quick look at the manual, it looks like you are supposed to use just the wrapper, not combine the wrapper with a shell. Can you show me an example of such combined usage?
  The error seems to suggest that the wrapper already has a shell directive that you shell conflicts with.
  
original_text: 14547: <p>I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error &quot;Multiple run or shell keywords in rule run_fastqc&quot;.</p>
  <p>Snakefile:</p>
  <pre><code>rule run_fastqc:
      input:
          &quot;/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz&quot;
      output:
          &quot;./[out path]/well01_S001_L001_R1_001.fastqc.html&quot;,
          &quot;./[out path]/well01_S001_L001_R1_001.fastqc.zip&quot;
      wrapper:
          &quot;0.79.0/bio/fastqc&quot;
      shell:
          &quot;fastqc {input} --outdir=./[out path]/&quot;
  </code></pre>
  <p>I've also tried:</p>
  <pre><code>...
      shell:
          &quot;fastqc {input} -o ./[out path]/&quot;
  ...
      shell:
          &quot;fastqc -o ./[out path]/ {input}&quot;
  ...
      shell:
          &quot;fastqc {input}&quot;
          &quot;fastqc -o ./[out path]/&quot;
  ...
      shell:
          &quot;fastqc {input} &gt; -o ./[out path]/&quot;
  </code></pre>
  <p>Code:</p>
  <pre><code>snakemake --cores 1 well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip
  </code></pre>
  <p>Output:</p>
  <pre><code>SyntaxError in line 9 of /[path to Snakefile]/Snakefile:
  Multiple run or shell keywords in rule run_fastqc. (Snakefile, line 9)
  </code></pre>
  <p>When I run fastqc alone (not in snakemake), it works and I get the two output files. How can I get snakemake to work?</p>
  <p>Thank you for your time and help!</p>
   650: <p>From a quick look at the manual, it looks like you are supposed to use just the <code>wrapper</code>, not combine the <code>wrapper</code> with a <code>shell</code>. Can you show me an example of such combined usage?</p>
  <p>The error seems to suggest that the wrapper already has a <code>shell</code> directive that you <code>shell</code> conflicts with.</p>
  