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populationgenomics / production-pipelines

Genomics workflows for CPG using Hail Batch
MIT License
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Issue 717 analysis meta #718

Closed MattWellie closed 1 month ago

MattWellie commented 2 months ago

Partially Addresses #717

Sorry y'all, tagging you both on a fairly early stage PR. 2 commits here (so far):

  1. removes the transcription of full QC reports into the meta
  2. pops the SG ID list off before writing the analysis entry meta - this is done right at the end, just in case SG IDs are re-populated by any of the update_meta callables. The job attribute dicts will still contain the SG IDs, but they might be used for billing purposes and I don't want to interfere with that.

Shoved in a bunch of get_config -> config_retrieve with defaults. Unrelated to this issue, but y'know... Passes the time

MattWellie commented 1 month ago

Pertinent to #728, all the _update_meta methods which directly create a CloudPath instance are flagged as MyPy failures

Cannot instantiate abstract class
"CloudPath" with abstract attributes "drive", "is_dir", "is_file", "mkdir" and
"touch"

fixable, ignorable, but if we're going to stop doing this anyway we should probably delete these methods that are writing whole QC reports into the analysis.meta