Nils Homer

FWIW: snakemake activates conda environments for you ;P

Here's how I fixed it with my local miniWDL install: https://github.com/chanzuckerberg/miniwdl/pull/569

@mlin thanks for the fix in 2c8df3c. Any thoughts on a `conda` directive?

Chiming in that I hit this too, and using the "legacy osxfs files sharing" fixed it for me too.

Also, when giving an explicit job definition on AWS, it shows the job definition not the container:

Re-opened to suggest that @pd3 explicitly state that a “.” value should not be interpreted one way or the other.

What about if we use the secondary's alignment information along with the next primary segment's alignment information to compute TLEN, almost as though viewing TLEN from the "secondary alignment" 's...

I am happy to remove `/1` and `/2`. What additional things need for this to be approved?

> Is this something that only fgbio does, or do other workflows heavily using MI do something similar? What do MI values typically look like, both as generated by fgbio...

~~Looks like the link to the PDF from the bot is broken :/~~ Fixed by a preview of the upcoming GitHub Actions-based robot (see jmarshall/hts-specs#3).