Decide on code formatting standards about long-read-pipelines HOT 5 CLOSED

For WDL

• should we use tabs vs spaces
• if using spaces, should we use 2 or 4

from long-read-pipelines.

We should come up with standards for Docker images as well. For example, make sure installed tools reside on the PATH. I just tripped myself up with two docker images of mine that had the same tool installed, but in different locations, and that seems silly.

from long-read-pipelines.

Agree.
Regarding dockers, I actually prefer not aggregating tools into a single docker, unless it is something very very basic like samtools, gsutils, etc.
And when the pipeline gets complicated, the docker DAG gets complicated as well, but I have a way to manage that to balance out build time, docker size (not that big of a deal for long reads yet because we won't have 10k samples), and complexity.

from long-read-pipelines.

I think we've more or less converged on decent rules for our WDL files and Docker images.

WDL:

• spaces, not tabs
• tab = 4 spaces

Docker images:

• prefer many small images over monolithic images
• prefer standalone images over bunch of images that depend on each other and need to be built in a specific order to function properly

from long-read-pipelines.

I'd vote for codifying these in a document.
I'll draft another document for this.

from long-read-pipelines.