dsl2: metagenomics uncollapsed paired end #1098

Draft

ilight1542 wants to merge 7 commits intodevfrom metagenomics-pairedend

+215-131

Commits on Sep 13, 2024

partial fix for krakenuniq, error within kraken call for PE (thinks fasta?)
ilight1542
committed

Commits on Oct 4, 2024

notes for fixes going forward
ilight1542
committed

Commits on Oct 18, 2024

added warning, and correct parsing for input into metagenomic screening for PE vs SE
ilight1542
committed

Commits on Oct 25, 2024

Commits on Nov 15, 2024