looper
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pepkit
A job submitter for Portable Encapsulated Projects
I'm trying to submit 6 jobs with looper. I've never submitted any before, it's a brand new project. I noticed one of them says: > Found existing status: completed. Skipping...
Can't looper destroy something. Related to #459. and also #464 -- these things should have been caught by testing. ``` looper destroy --sel-incl demo4 Looper version: 1.7.0 Command: destroy Using...
Say I run a sample through a pipeline that uses pipestat. Now say I want to clear out that sample and re-run it. I call `looper destroy` and use the...
If I run a job and it fails, it creates a "_failed.flag", correctly. When I try to do `looper run`, it won't run these because they have failed flags --...
How do you configure the pipestat pipeline name when passing it via looper? Here's my looper config; ``` pep_config: demo_fasta.yaml output_dir: results pipeline_interfaces: sample: ../pipeline/pipeline_interface.yaml pipestat: project_name: demo results_file_path: results/pipeline_stats.yaml...
As we've discussed, looper should be adapted to use `FutureYAMLConfigManager` from yacman `v0.9.3`
I'm unsatisified with how long it takes the `looper` CLI to run. I guess it's because looper imports a bunch of heavy stuff, like `pandas`, `peppy`, `sqlalchemy` (via pephubclient), etc....
Right now we have `var_templates` in the pipeline interface, which populates jinja templates. These are useful to provide parameters to plugins, but the names can potentially clash since they're not...
I find the current documentation on how to configure a new project with looper to be really difficult. There are basically 2 problems: 1. the documentation is outdated and incomplete....
It's unclear why the pipeline type is specified both in the pipeline interface and the looper config
Right now, a pipeline interface can say `pipeline_type: sample` or `pipeline_type: project`. Then, in the `.looper.yaml`, you say something like: ``` pipeline_interfaces: sample: ../pipeline/pipeline_interface.yaml ``` So, you're specifying the type...