Add bamCompare support and robust BWA index resolution to ChIP-seq workflow

[WilliamLautertD]

Motivation

• Add automatic ChIP vs Input ratio bigWig generation (bamCompare) so ChIP samples can be directly compared to their paired Input controls.
• Make control/Input pairing explicit in the sample sheet to avoid ambiguous pairing and to fail early when a control is missing.
• Improve reference resolution so the workflow accepts either a BWA index basename or a FASTA and will auto-detect common .fa basenames and warn if it auto-corrects a relative path.

Description

• Introduced a new BAM_COMPARE process that runs bamCompare with --ignoreDuplicates, --operation ratio, configurable --binSize and --smoothLength, and publishes ratio bigWigs to coverage/bamcompare.
• Added new params in chipseq_nextflow.config: make_bamcompare, bamcompare_binsize, and bamcompare_smooth_length, and allocated withName: BAM_COMPARE CPUs.
• Updated chipseq_samples.tsv template to include a control_sample column and updated the workflow to require a control_sample for non-Input conditions, storing it in meta.control_sample.
• Implemented resolveBwaReference() and validateBwaReference() helper functions that locate BWA index files (.amb/.ann/.bwt/.pac/.sa) for a given basename or try .fa variants, set params.bwa_resolved_reference, and emit a warning if the path was auto-corrected.
• Updated BWA_MEM_FILTER to use params.bwa_resolved_reference (or fall back to resolveBwaReference()), and added workflow wiring that joins chip sample BAMs with their Input BAMs and conditionally invokes BAM_COMPARE when params.make_bamcompare is enabled.
• Documentation tweaks in README.md to document the control_sample pairing, bwa_index_prefix expectations, and bamCompare defaults.

Testing

• No automated tests were run for this change.

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Codex Task