Option to extract columns from the TSV before compressing and indexing it

[muffato]

A PR to address sanger-tol/sequencecomposition#47 (comment)

Jim made me realise that there's no need to have the patch in my pipeline since the module is from sanger-tol.

This adds optional parameters in BGZIPTABIX to cut certain columns and skip some header lines from the TSV, as well as updating the extension.

PR checklist

Closes #XXX

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[Copilot]

Pull request overview

Adds optional pre-processing to the BGZIPTABIX module so it can (optionally) extract specific columns and skip header lines from tab-delimited inputs (e.g. converting TSV → BED) before bgzipping and indexing, and updates downstream usage/tests accordingly.

Changes:

• Extend BGZIPTABIX to accept column_numbers, header_lines, and extension inputs and use them to transform data before bgzip/tabix.
• Update SOFT_MASKED_FASTA_REPEATS to pass the new (optional) parameter tuple into BGZIPTABIX.
• Add a new module test covering TSV→BED extraction and update snapshots.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
subworkflows/sanger-tol/soft_masked_fasta_repeats/main.nf	Updates BGZIPTABIX invocation to supply the new optional parameter tuple.
modules/sanger-tol/bgziptabix/main.nf	Implements optional cut/header-skip behavior and output extension override before bgzip/tabix.
modules/sanger-tol/bgziptabix/meta.yml	Documents the new optional inputs for column extraction, header skipping, and output extension.
modules/sanger-tol/bgziptabix/tests/main.nf.test	Updates all tests for the new input signature and adds a TSV→BED test.
modules/sanger-tol/bgziptabix/tests/main.nf.test.snap	Updates snapshots to reflect the new test and outputs.

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