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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
20 stars 7 forks source link

summarizer command should be called once per pipeline #217

Closed nsheff closed 4 years ago

nsheff commented 5 years ago 
[2019-08-26 14:17:31,066] {looper:591} (get_jinja_env) [DEBUG] > Using templates dir: /home/nsheff/.local/lib/python2.7/site-packages/looper/jinja_templates 
[2019-08-26 14:17:31,071] {looper:388} (create_status_html) [DEBUG] > Building status page... 
[2019-08-26 14:17:31,086] {looper:394} (create_project_objects) [DEBUG] > Building project object... 
[2019-08-26 14:17:31,087] {looper:437} (create_project_objects) [WARNING] > Summarizer was unable to find: Library complexity file (summary/ppqc_libComplexity.pdf) 
[2019-08-26 14:17:31,088] {looper:437} (create_project_objects) [WARNING] > Summarizer was unable to find: Library complexity file (summary/ppqc_libComplexity.pdf) 
[2019-08-26 14:17:31,103] {looper:748} (_read_tsv_to_json) [DEBUG] > Reading TSV from '/ext/yeti/processed/ppqc_test/ppqc_test_stats_summary.tsv' 
[2019-08-26 14:17:31,141] {looper:488} (__call__) [INFO] > HTML Report (n=4): /ext/yeti/processed/ppqc_test/ppqc_test_summary.html
nsheff commented 5 years ago

it's because there were two protocols in this project, which I guess is intended behavior...

nsheff commented 5 years ago

Actually, this is a problem... we should ultmiately call the summarizer one per pipeline, not once per protocol... in the case of peppro, where a project has GRO and PRO samples, the summerizer is being called twice, but should only be called once.

So we should first go through the protocols and get all the relevant pipelines, then loop through the set of pipelines.