possible to split stderr and stdout

[Sam-Sims]

Currently doing something like

squarepeg run quay.io/biocontainers/minimap2:2.31--h118bc1c_0 minimap2 \
-ax map-ont blah.fasta \
blah.fastq.gz > mapped.sam

will output a sam file with stderr and stdout combined, thus the sam file becomes unusable

(I can do -o mapped.sam) but would be nice if there was an option to split

[Sam-Sims]

Actually wasnt sure if the k8 API even supports this - did some searching (should of done that before opening an issue :D) and turns out it does but only very recently and is an alpha feature disabled by default

Im using 1.27 (on climb) - so looks like wouldnt be possible currently anyhow

Would be good to have as a feature if a cluster did enable this though

[BioWilko]

Yeah it's something I'll directly support when CLIMB does :)