Using `looper runp` for PEPATAC Collator with Looper pre-release (1.6.0) results in errors

[donaldcampbelljr]

When using looper runp for PEPATAC Collator:

Error populating command template: 'dict object' has no attribute 'looper'
> Not submitted: 'dict object' has no attribute 'looper'

project pipeline interface:

pipeline_name: PEPATAC_summarizer
pipeline_type: project
path: pipelines/pepatac_collator.py
output_schema: pepatac_output_schema.yaml
command_template: >
  {pipeline.path} 
  --config {looper.pep_config}
  -O {looper.output_dir}
  -P {compute.cores}
  -M {compute.mem}
  -n {project.name}
  -r {looper.results_subdir}
compute:
  singularity_image: ${SIMAGES}pepatac
  docker_image: databio/pepatac
  bulker_crate: databio/pepatac:1.0.10
  size_dependent_variables: resources-project.tsv

bioconductor:
  readFunName: readPepatacPeakBeds
  readFunPath: BiocProject/readPepatacPeakBeds.R

During looper's command template rendering, I notice that the Looper namespace is actually a YAMLConfigManager not a dict.

The project variable {project.name} renders fine and it is a simple dict.

[donaldcampbelljr]

This is a looper issue since the rendering is happening there.

[donaldcampbelljr]

runp is still giving an error but it appears that it is due to this issue: https://github.com/databio/pepatac/issues/254

Therefore, closing this issue for now.