Looper: missing argument error 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.
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.