<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>

CC BY-SA 3.0
2018-01-18T12:36:06.103Z
2018-01-18T12:36:06.103Z
nsheff
<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>

<scrnaseq><yaml><looper>
Looper: missing argument error
# Looper: missing argument error

(Asked by: username_0 on 2018-01-18)

While trying to run 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

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## 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/).


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