Implement unclassified reads extraction in sequana_taxonomy

[cokelaer]

Summary

• Extract unclassified reads from Kraken output instead of creating empty placeholder file
• Support both paired-end and single-end input sequences
• Properly cleanup temporary files after merging paired reads

Changes

• Updated test Snakefile to expect unclassified output in correct kraken/ subdirectory
• Implemented proper seqkit grep extraction pipeline for unclassified reads
• Handle paired-end by extracting both R1 and R2 reads then concatenating
• Handle single-end by direct extraction to output file
• Cleanup temporary unclassified ID list and intermediate files

Test Plan

• Run test in sequana_wrappers/shells/sequana_taxonomy/run/test/
• Verify unclassified reads extracted correctly for paired-end input
• Verify unclassified reads extracted correctly for single-end input
• Verify output file at correct path kraken/unclassified.fastq

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[codacy-production]

Not up to standards ⛔

🔴 Issues 2 medium · 1 minor

Alerts:
⚠ 3 issues (≤ 0 issues of at least minor severity)

Results:
3 new issues

Category	Results
Security	2 medium 1 minor

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🟢 Metrics 14 complexity · 0 duplication

Metric	Results
Complexity	14
Duplication	0

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