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New EPP Adjust missing reads for sequencing #515

Merged

Karl-Svard merged 16 commits into master from sequencing_pooling_adjustments

Sep 3, 2024

Contributor

idalindegaard commented Jul 17, 2024 •

edited by Karl-Svard

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Linked to lims issue 514

Added

New script: adjust_missing_reads.py in epps > udf> calculate
Updated options.py
Updated base.py in epps > udf> calculate

Changed

Fixed

Steps to consider while deploying

Configuration changes:
Documentation updates:
Inform users by email:

Review:

Code approved by
Tests executed on stage by: (Document the test done with screen shots and description.)
"Merge and deploy" approved by

This version is a:

MAJOR - when you make incompatible API changes
MINOR - when you add functionality in a backwards compatible manner
PATCH - when you make backwards compatible bug fixes or documentation/instructions

idalindegaard added 2 commits

June 13, 2024 12:54


          New script and updated file

3a2475c


          New EPP adjust missing reads

dc3aeeb

idalindegaard requested review from Karl-Svard and amandaraud as code owners

July 17, 2024 08:59

idalindegaard mentioned this pull request

New EPP to adjust the sequencing reads for samples in Define Run Format and Calculate Volumes (NovaSeq X) #514

Closed

6 tasks


          updated validate_udf_values

afc2162

idalindegaard requested a review from AbiDalby as a code owner

August 21, 2024 08:44

idalindegaard added 2 commits

August 21, 2024 11:51


          update validate_udf_values

92cc190


          update validate_udf_values

b8e81eb

Contributor Author

idalindegaard commented Aug 22, 2024

Testing was documented in LIMS issue 514

Karl-Svard added 2 commits

August 29, 2024 14:04


          Format with black and isort

54ff59c


          remove unused imports and variables

4bd84c5

Karl-Svard reviewed

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idalindegaard and others added 9 commits

August 29, 2024 16:40


          Update cg_lims/EPPs/udf/calculate/adjust_missing_reads.py

a1c35bd

Co-authored-by: Karl Svärd <[email protected]>


          Update cg_lims/EPPs/udf/calculate/adjust_missing_reads.py

23d3ba8

Co-authored-by: Karl Svärd <[email protected]>


          Update adjust_missing_reads.py

49c5e65

- Added type hints
- removed unused variable in function adjust_reads
- renamed variable reset_microbial_reads to reset_reads so it wouldn't have the same name as the function it was used in


          added some more type hints

5c22fe7


          restructure to decrease indentation

9f7fa23


          save apptag as variable

5c0ee40


          modified is_adjusted check slighty

2b70049


          added more logging


          refactored main function

19acb0b

Karl-Svard approved these changes

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Collaborator

Karl-Svard left a comment

Great work!! 🔥

Karl-Svard merged commit 65d8ea6 into master

2 checks passed

Karl-Svard deleted the sequencing_pooling_adjustments branch

September 3, 2024 09:43

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