Don't crash on missing options

Reintroducing $consensus, deleted (accidentally) at some point in the past

expect as little as two lines in checkm2 output, fixes #1013

Update 04.rundiamond.pl

-_-'

Update README.rst

auto version docs

add sqmtools build instructions

add to exportPathway

make bin abundance recalculation dependent on , improve behaviour of

CRAN compat and fix error in subsetSamples

prepare for release

make sqm_reads/longreads work with absolute project paths, fix #586

Fix wrong percent calculation by subsetFun when working on subsets, fixes #982

transform extassembly ans extbins into proper modes