Use samtools import for FASTQ to BAM conversion with validated barcode extraction (fastq_to_ubam.nf only)#49

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Copilot wants to merge 18 commits into

copilot/fix-fastq-bam-header-parsing

Commits on Jan 24, 2026

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Copilot
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Fix barcode extraction to handle non-standard FASTQ headers

Copilot
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bwlang
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Refactor: Extract duplicate barcode extraction logic to shared function

Copilot
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bwlang
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Add tests for barcode extraction with non-standard headers

Copilot
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bwlang
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Revert changes to legacy/em-seq.nf workflow

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bwlang
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Add comprehensive documentation to extractBarcode function

Copilot
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bwlang
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Fix test: correct glob pattern and BAM filename for standard barcode extraction test

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bwlang
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Fix test glob pattern to match fromFilePairs expectations

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bwlang
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Simplify tests to only check workflow success and file existence

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bwlang
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Output barcode values to text files and verify them in tests

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bwlang
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Commits on Jan 25, 2026