Add pair_mode column to tasmanian output (read vs insert)

[aerijman]

Adds pair_mode column to tasmanian output, distinguishing read vs insert level positional counts.

[Copilot]

🟡 Changes recommended

Critical integration and failure-handling issues, plus output, resource, and test contract problems, remain unresolved.

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Pull request overview

This PR adds read- and insert-level Tasmanian positional counts with a pair_mode column.

Changes:

• Runs Tasmanian in read and insert modes.
• Combines results into a TSV with mode labels.
• Updates dependencies, inputs, and process configuration.

File summaries

File	Review findings
modules/tasmanian.nf	Critical (3): Required inputs are not wired correctly; the FAI is passed as a mask bedgraph. Output emit name mismatches the caller. Failures may be masked by disabled error propagation. Moderate (3): process_low lacks a configured selector. Moderate (2): Publication and filename changes break the existing output contract. Nit (1): Tests do not validate the new pair_mode values.

Review details

Suppressed comments (1)

modules/tasmanian.nf:45

• The new read/insert merge is not covered by the existing nf-tests: they still look for *.tasmanian.csv and only assert file existence, rather than checking the new header and read/insert values. Update both test cases and snapshots to the .tsv path and assert representative rows contain the new pair_mode values, otherwise this behavior can regress unnoticed.

	head -n1 ${library}.tasmanian.read.tsv | awk '{print $0"\tpair_mode"}' > ${library}.tasmanian.tsv 
	tail -n +2 ${library}.tasmanian.read.tsv | awk '{print $0"\tread"}' >> ${library}.tasmanian.tsv
	tail -n +2 ${library}.tasmanian.insert.tsv | awk '{print $0"\tinsert"}' >> ${library}.tasmanian.tsv

• Files reviewed: 1/1 changed files
• Comments generated: 5
• Review effort level: Lite

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