wanted: janis wait

[drtconway]

Hi Janis,

It'd be really nice to have a command

janis wait myworkflowid

which waits until the referenced workflow completes.

Bonus marks:

• exit code reflects status of workflow in case of failure.
• multiple workflows can be waited.
• option to restart failed workflows up to some specified number of times
• make a file with the id of the current run outputdir/janis/id to make it easy to get the id of the run of interest. It could do one line per attempted run so you can use tail to git the run you want to examine.

Partial credit:

• implement it as janis watch --silent myworkflowid

Motivation

For reasons of practicality, I have multiple workflows for different parts of a project: alignment, variant calling, copy number, etc. These also get run on different inputs.

It would be nice to be able to write a simple shell script that at least in theory can rerun them all. Assuming no failures, this would make a relatively simple way to document the overall workflow for a large project.

I guess in you could kind of run

janis watch myworkflowid > /dev/null 2>&1

but that almost certainly does quite a lot more work than necessary.

[illusional]

Implemented and released in v0.11.0, where wid below is the workflow ID or the execution path (usually <output-dir>/janis):

$ janis wait --help
usage: janis wait [-h] wid [wid ...]

positional arguments:
  wid         Workflows to wait for

optional arguments:
  -h, --help  show this help message and exit

Example:

janis wait /path/to/workflow1/janis aed123d

This exits with rc=3 if any of the workflows to watch fail.