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Y24-035 tnanoseq update configs for pipeline #1711

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merged 17 commits into from
Jul 25, 2024

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Closes #1646

Changes proposed in this pull request

Updates config to allow Targeted NanoSeq to use ReISC and to loop with submissions.

@andrewsparkes andrewsparkes self-assigned this May 24, 2024
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codecov bot commented May 24, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.43%. Comparing base (d347ec1) to head (eaac64f).

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #1711      +/-   ##
===========================================
+ Coverage    91.38%   91.43%   +0.04%     
===========================================
  Files          373      373              
  Lines         7686     7714      +28     
===========================================
+ Hits          7024     7053      +29     
+ Misses         662      661       -1     
Flag Coverage Δ
javascript 93.65% <ø> (ø)
pull_request 91.43% <100.00%> (?)
push 91.43% <100.00%> (+0.04%) ⬆️
ruby 91.12% <100.00%> (+0.05%) ⬆️

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@yoldas yoldas left a comment

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Looks good.

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@yoldas yoldas left a comment

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The latest changes for allowing to leave rows in file but set pic_cycles to 1 to ignore them look good. I have inserted binding.pry in several places and inspected the changes as well. The update clearly excludes rows with pcr_cycles set to 1 before comparing active requests and customer file wells, for validations. There are enough code comments.
Type info in comments, params, returns would make them better.

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codeclimate bot commented Jul 4, 2024

Code Climate has analyzed commit eaac64f and detected 2 issues on this pull request.

Here's the issue category breakdown:

Category Count
Complexity 2

The test coverage on the diff in this pull request is 100.0% (50% is the threshold).

This pull request will bring the total coverage in the repository to 91.1% (0.0% change).

View more on Code Climate.

@andrewsparkes andrewsparkes merged commit bcd08d7 into develop Jul 25, 2024
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@andrewsparkes andrewsparkes deleted the y24-035-tnanoseq-update-configs-for-pipeline branch July 25, 2024 14:33
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Y24-035 Targeted NanoSeq - update configuration for pipeline and add submission for ISC prep
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