Dev test new looper, pypiper, pipestat - Githubissues

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

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Dev test new looper, pypiper, pipestat #255

Closed donaldcampbelljr closed 11 months ago

donaldcampbelljr commented 1 year ago

Align PEPATAC to use newest versions of:

[x] pipestat 0.6.0
[x] looper 1.6.0
[x] pypiper 0.14.0

Current changes include:

PEPATAC now reports results to a single pepatac_results.yaml file instead of a separate stats.yaml for each sample. This single results file is required for pipestat configuration via looper so that looper report and looper link will work. See: https://github.com/databio/pepatac/issues/257 and https://github.com/databio/pepatac/issues/256
The output_schema is now a pipestat output_schema (adhering to JSON schema)

WIP

[x] pypiper's get_stat must be modified so that results can be read (currently the pipeline fails with more than one sample reported) See: https://github.com/databio/pypiper/issues/202
[x] PEPATAC reports results that are not in the output schema. This means that they are not captured in the HTML report when using looper report

donaldcampbelljr commented 11 months ago

Merging to dev and then master for newest looper, pypiper, and pipestat releases.