Donald Campbell

Playing around with bulker, I unloaded all my crates and then confirmed via `bulker list`. However, bulker throws an error: ``` bulker list Using default config. You may specify in...

Make suggested changes to `looper init`

4

- [x] remove pause. - [x] it currently erroneously complains if you give it a registry path. - [x] remove asking if the user would wish to follow tutorial (assume...

- [ ] Ensure docs are updated: https://github.com/pepkit/pepspec/pull/34

Remove printed dict at looper finish

1

Currently looper prints a statement in dict format for the commands/jobs submitted: ``` Looper finished Samples valid for job generation: 2 of 2 {'Pipestat compatible': False, 'Commands submitted': '2 of...

how do to parallel-process files with looper locally -- lump them together, this will group several commands in one like:

1

> how do to parallel-process files with looper locally -> originally a divvy idea. > issue: 100 files -> divvy submits to cluster no problem, if local they will run...

For Looper 2.0, we will consolidate sample and project level pipeline interfaces under a single interface. This will break backwards compatibility. ```yaml pipeline_name: example_pipestat_pipeline output_schema: pipestat_output_schema.yaml sample_interface: command_template: > python...

After discussion, we would like to merge Eido back into Peppy as well as add some functionality to validation. Currently, Eido primarily validates post-processed PEPS. However, it may be useful...

Using preseq 3.2.0 with BAM as input

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Hello, One of our pipelines currently uses preseq 2.0 and uses BAM files as an input to preseq. I recently attempted to upgrade to 3.2.0 and, after following the instructions...

I noticed in the refactored hello looper examples that `looper report` seems to call pipestat summarize multiple times (seemingly once per sample): ``` (venv) drc@databio:~/GITHUB/hello_looper/hello_looper/pipestat_example$ looper report --portable Looper version:...