Answers.Body: <p>You are using the argument values incorrectly. Argument values are sample attributes, not full character paths. Hence, "IU" is a sample attribute, "gencode_mouse_m13" is a sample attribute, so why would you think "/scratch..." would be treated any differently?</p>
  
  <p>The pipeline interface maps sample attributes to command-line arguments. It is modulated by sample (different values per sample). What you're trying to do is pass a constant string to an argument.</p>
  
  <p>For this, there is a <code>pipeline_args</code> section of your project config. Please read the docs on <a href="https://pepkit.github.io/docs/project_config/" rel="nofollow noreferrer">project config</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-18T12:36:06.103Z
Answers.LastActivityDate: 2018-01-18T12:36:06.103Z
Answers.UserDisplayName: nsheff
Body: <p>While trying to run <a href="https://github.com/pepkit/looper" rel="nofollow noreferrer">looper</a> I am getting the following error:</p>
  
  <blockquote>
    <p>Error (missing attribute): 'sandro_rna_seq' requires sample attribute '/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-metadata.yaml' for option/argument '-E'<br>
    Not submitted: Required attribute(s) missing for pipeline arguments string</p>
  </blockquote>
  
  <p>In my <code>pipeline_interface.yaml</code> file I have the following:</p>
  
  <pre><code>arguments:
    "-L": "IU"
    "-T": "gencode_mouse_m13"
    "-E": "/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-
  metadata.yaml"
  </code></pre>
  
  <p>The file <code>"/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-metadata.yaml"</code> is definitely present but it still gives an error...</p>
  
  <p>Any suggestions would be greatly appreciated.</p>
  
Tags: <scrnaseq><yaml><looper>
Title: Looper: missing argument error
ThreadText: # Looper: missing argument error
  
  (Asked by: username_0 on 2018-01-18)
  
  While trying to run [looper](https://github.com/pepkit/looper) I am getting the following error:
  
  > Error (missing attribute): 'sandro\_rna\_seq' requires sample attribute '/scratch/nv4e/sandro\_looper/pipeline/jyvo\_experiment-metadata.yaml' for option/argument '-E'  
  > Not submitted: Required attribute(s) missing for pipeline arguments string
  
  In my `pipeline_interface.yaml` file I have the following:
  
  ```
  arguments:
    "-L": "IU"
    "-T": "gencode_mouse_m13"
    "-E": "/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-
  metadata.yaml"
  
  ```
  
  The file `"/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-metadata.yaml"` is definitely present but it still gives an error...
  
  Any suggestions would be greatly appreciated.
  
  **Tags:** scrnaseq, yaml, looper
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-01-18. Score: 2 | Accepted answer
  
  You are using the argument values incorrectly. Argument values are sample attributes, not full character paths. Hence, "IU" is a sample attribute, "gencode\_mouse\_m13" is a sample attribute, so why would you think "/scratch..." would be treated any differently?
  
  The pipeline interface maps sample attributes to command-line arguments. It is modulated by sample (different values per sample). What you're trying to do is pass a constant string to an argument.
  
  For this, there is a `pipeline_args` section of your project config. Please read the docs on [project config](https://pepkit.github.io/docs/project_config/).
  
  
  ---
  
  