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Make nominal_length and nominal_sdev optional in experiments#26

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misialq merged 6 commits intobokulich-lab:mainfrom
ZuzanaSebb:main
Feb 26, 2026
Merged

Make nominal_length and nominal_sdev optional in experiments#26
misialq merged 6 commits intobokulich-lab:mainfrom
ZuzanaSebb:main

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@ZuzanaSebb
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Hi @misialq,

I’ve removed nominal_length and nominal_sdev from the mandatory experiment parameters, in line with the SRA XML schema.

I updated library.py and test_library.py accordingly.

Regarding the provided experiment templates, I only modified experiment_minimal.tsv to reflect these changes. The extended templates for single and paired reads remain unchanged. The minimal template uses paired reads by default, so users can follow it without specifying nominal_length or nominal_sdev.

@ZuzanaSebb ZuzanaSebb linked an issue Jan 27, 2026 that may be closed by this pull request
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codecov bot commented Feb 19, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.13%. Comparing base (bc68788) to head (6cd2124).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #26      +/-   ##
==========================================
+ Coverage   95.07%   95.13%   +0.05%     
==========================================
  Files          27       27              
  Lines        1788     1808      +20     
==========================================
+ Hits         1700     1720      +20     
  Misses         88       88              

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@ZuzanaSebb ZuzanaSebb force-pushed the main branch 2 times, most recently from 6bf43cf to e4387e4 Compare February 23, 2026 09:47
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@misialq misialq left a comment

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Hey @ZuzanaSebb, thanks for the updates - LGTM! 🔥

@misialq misialq merged commit 63de51c into bokulich-lab:main Feb 26, 2026
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Do not require NOMINAL_LENGTH / NOMINAL_SDEV for paired libraries

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