modkit: sample 50000 reads for mt-scope thresholds

modkit estimates the pass threshold from a sample of reads (default 10042). The human
blood barcodes hold 100 to 500 MT reads, so the estimate used every read and was
deterministic; the mouse hippocampus mice hold 3000 to 16000 chrM reads, and above
the default the estimate becomes a non-reproducible subsample. sample-probs, pileup
and summary now pass --num-reads ${params.modkit_num_reads} (50000) so every MT
read enters the estimate whatever the depth. Rationale and the provenance note on
the archived human runs (called with the earlier fixed 0.75 threshold) are in
docs/pipeline_notes.md#modkit.

Co-Authored-By: Claude Fable 5.1 <[email protected]>