Answers.Body: <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>
  
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Answers.Text: Thank you! In Output, I also had to remove the "./[out path]/" before the output file name, I guess the "--outdir" in Shell is sufficient. I got the files but still received the error: "Job Missing files after 5 seconds:
  well01_S001_L001_R1_001.fastqc.html
  well01_S001_L001_R1_001.fastqc.zip
  This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
  Job id: 0 completed successfully, but some output files are missing. 0" and I also waited for 60s and got the same error.
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Body: <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>
  
Tags: <rna-seq><python><snakemake><quality-control><fastqc>
Title: Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."
ThreadText: # Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."
  
  (Asked by: username_0 on 2021-11-11)
  
  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!
  
  **Tags:** rna-seq, python, snakemake, quality-control, fastqc
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-11-11. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: Thank you! In Output, I also had to remove the "./[out path]/" before the output file name, I guess the "--outdir" in Shell is sufficient. I got the files but still received the error: "Job Missing files after 5 seconds: well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 0 completed successfully, but some output files are missing. 0" and I also waited for 60s and got the same error.  
  
  ---
  
  