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Previously TACA set the base mask to N0 if the recipe in the LIMS sample manifest was 0 for a read or index but this is not accepted by bases2fastq. Instead, it should be set to N* (or alternatively not specified in the manifest).

For a manifest with the recipe 64-6-0-0, the TACA will now make a manifest with the following settings section:

[SETTINGS]
SettingName, Value
R1FastqMask, R1:Y64
I1Mask, I1:Y6
I2Mask, I2:N*
R2FastqMask, R2:N*

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codecov bot commented Feb 3, 2026

Codecov Report

❌ Patch coverage is 0% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 26.14%. Comparing base (3e58339) to head (faaa451).
⚠️ Report is 6 commits behind head on master.

Files with missing lines Patch % Lines
taca/element/Element_Runs.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##           master     #501   +/-   ##
=======================================
  Coverage   26.14%   26.14%           
=======================================
  Files          37       37           
  Lines        5587     5587           
=======================================
  Hits         1461     1461           
  Misses       4126     4126           

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@ssjunnebo ssjunnebo requested review from FranBonath and aanil February 3, 2026 13:16
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👍

@ssjunnebo ssjunnebo merged commit 96923e3 into NationalGenomicsInfrastructure:master Feb 4, 2026
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2 participants