Mike Lin

Cromwell doesn't object to a workflow with the same name as a task in the same WDL file, while miniwdl does. We can probably relax. WDL spec may need clarification.

docker tasks occasionally hang when worker goes down

3

We've seen docker service tasks sporadically get stuck in the 'preparing' or 'assigned' [states](https://docs.docker.com/engine/swarm/how-swarm-mode-works/swarm-task-states/) indefinitely. This was under stress-testing, with rapid task turnover in a multi-node swarm, with occasional random...

cf. https://cromwell.readthedocs.io/en/develop/backends/TES/

option for task /tmp mount

2

If the task command needs to use scratch disk space intensively (to create big files not meant to be output), it's suboptimal to do so either (i) in the initial...

let task output files outside its working directory

2

Right now the task runtime doesn't allow output files that reside outside of the initial working directory or a subdirectory thereof; for example, attempting to output a file under /tmp...

This isn't really a miniwdl bug, but documenting it here as it's going to bite someone sometime. [There is a problem in the Python 3.3-3.6 `subprocess` implementation](https://bugs.python.org/issue25942) where if the...

Cromwell allows a scatter variable name to collide with another value elsewhere in the workflow. Inside the scatter body, the scatter variable shadows the other value. e.g. this is fine:...

htsget: add `samples` query parameter, principally to select subset of VCF columns

5

e.g. ``` GET /htsget/1000genomes/variants?format=VCF&samples=NA12878,NA12877 ``` Previously I circulated a different version of this with a repeated `sample=x` query parameter. This single, comma separated list is more consistent with the existing...