sample yaml paths

[nsheff]

in the current docs, the parameters for all the included plugins look like they specify the folder of where the yaml will be stored, but not the filename. Shouldn't the customizable path be to the filename rather than just a folder? otherwise, how do you know/customize the actual path?

For instance it says:

"If the parameter is not provided, the file will be saved in {looper.output_dir}/submission."

It should instead say: " If the parameter is not provided, the file will be saved in {looper.output_dir}/submission/{sample.sample_name}.yaml.

Instead of:

pipeline_type: sample
var_templates:
  main: "{looper.piface_dir}/pipelines/pipeline1.py"
  sample_yaml_path: "{looper.output_dir}/custom_sample_yamls"

it should say:

pipeline_type: sample
var_templates:
  main: "{looper.piface_dir}/pipelines/pipeline1.py"
  sample_yaml_path: "{looper.output_dir}/custom_sample_yamls/{sample.sample_name}.yaml"

right?

[stolarczyk]

well, the docs represent actual plugins behavior. But I agree, we should make this more flexible. I'll make the relevant code changes.

[stolarczyk]

resolved in 46722c3cc3a349f01b7da75cb214d2e75e344ad2

[nsheff]

thanks.