DockerTimeout on AWS Batch

[sivkovic]

This issue happening sometimes because volume IO utilization is close to 100% while downloading and uploading files.
Error on AWS Batch:
DockerTimeoutError: Could not transition to created; timed out after waiting 4m0s
In this case whole nextflow job will fail.
Other manifestation of the same issue:
CannotInspectContainerError: Could not transition to inspecting; timed out after waiting 30s
In this case only some jobs are seen as failed on AWS Batch although they are successful.

Link to nextflow issue.

[sivkovic]

Fix for nextflow timeout on AWS Batch sivkovic/nextflow#1. Waiting for NF folks to review.

[evanbiederstedt]

Fix for nextflow timeout on AWS Batch sivkovic/nextflow#1. Waiting for NF folks to review.

@sivkovic would it make sense to do a PR directly to Nextflow?

[sivkovic]

Merged. Works with nextflow version 19.05.0-SNAPSHOT build 5075