search

microbiomedata / nmdc_automation

Prototype automation
2 stars 2 forks source link

add code to generate input.jsons for steps defined in workflows-mt.yaml #230

Open aclum opened 2 months ago

aclum commented 2 months ago

Depends on https://github.com/microbiomedata/nmdc_automation/issues/222

logic will need to be added to decide what workflow component to run for nmdc:MetatranscriptomeExpressionAnalysis.

nmdc:MetatranscriptomeExpressionAnalysis is a new class which doesn't have any existing scheduler logic. The code use all docs (being used by the ref integrity squad) or an aggregation will need to traverse from omics_processing_set to library_preparation_set records to determine which of the following to run Expression Analysis Antisense - if library_preparation_set.stranded_orientation ='antisense orientation' Expression Analysis Sense - if library_preparation_set.stranded_orientation ='sense orientation' Expression Analysis Nonstranded -if is_stranded = false else run Expression Analysis Sense (default for JGI libraries)

ssarrafan commented 2 months ago

222 is closed. Can this issue be completed today @mbthornton-lbl?

aclum commented 2 months ago

No, Michael's on vacation. Moving this to the next sprint.

ssarrafan commented 1 month ago

Two more weeks have gone by... any update on this issue @mbthornton-lbl

aclum commented 1 month ago

I'm going to backlog this. The MVP for metatranscriptomes is to use the workflows config, where only one Expression workflow is enabled at once, to set up the correct inputs.json instead of using this logic.

ssarrafan commented 3 weeks ago

Removing from sprint and adding backlog label again FYI @mbthornton-lbl @aclum