Mosdepth failure on contig mismatch between cram and fasta

[matthdsm]

Description of the bug

Mosdepth fails when there are unknown contigs in cram vs the reference fasta.
Mosdepth 0.3.12 silently skips unknown contigs, while 0.3.14 complains and fails

xref brentp/hts-nim@93ad654

options for fixes:

• downgrade to mosdepth 0.3.12 to regain functionality while working on a fix upstream
• introduce filtering step to remove unknown contigs
• realign "old" data before entering smallvariants

System information

nf-cmgg/smallvariants 1.13.2

[matthdsm]

fixed in #336