How to use the looper config file
Starting with looper
version >=1.5.0
, you should specify a pipeline interface in the looper config file, rather than in the PEP.
Example looper config file using local PEP:
pep_config: $HOME/hello_looper-master/project/project_config.yaml
output_dir: "$HOME/hello_looper-master/output"
pipeline_interfaces:
sample: ["$HOME/hello_looper-master/pipeline/pipeline_interface"]
project: "some/project/pipeline"
In addition, looper>=1.5.0 supports projects from PEPhub. Using a PEP from PEPhub allows a user to run a pipeline without downloading the PEP. This allows you to keep the sample table in a centralized, shared location. You need only specify all necessary environment variables used by the PEP.
Example looper config file using PEPhub project:
pep_config: pephub::databio/looper:default
output_dir: "$HOME/hello_looper-master/output"
pipeline_interfaces:
sample: ["$HOME/hello_looper-master/pipeline/pipeline_interface"]
project: "$HOME/hello_looper-master/project/pipeline"
Where:
- output_dir
is pipeline output directory, where results will be saved.
- pep_config
is a local config file or PEPhub registry path. (registry path should be specified in one
one of supported ways: namespace/name
, pephub::namespace/name
, namespace/name:tag
, or pephub::namespace/name:tag
)
- pipeline interfaces
is a local path to project or sample pipelines.
To run pipeline, go to the directory of .looper.config and execute command in your terminal:
looper run --looper-config {looper_config_path}
or looper runp --looper-config {looper_config_path}
.