[dependabot]

Bumps miniwdl from 1.15.0 to 1.16.0.

Release notes

Sourced from miniwdl's releases.

v1.16.0

Getting Started

miniwdl v1.16.0 is maintenance + one experimental feature.

⚠️ Python 3.10+ is now required, dropping 3.8 and 3.9. ⚠️ The default task container image (used when the task definition specifies none) advances to ubuntu:22.04 from 20.04.

• S3 downloads: with [aws] host_credentials = true, inherit the host's AWS region along with its credentials (#922 #818 @​ThomasHickman), and the S3 endpoint URL, enabling other S3-compatible object stores (#909 @​manutorresdiz).
• Fix select_all() result type when the first scattered element is null (#911 @​smlchen).
• Docker Swarm backend: don't mistake a container's exit code for an interruption (#918 #902 @​adamnovak).
• Replace pygtail dependency with a faster, unencumbered internal implementation (#915 @​markjschreiber).
• Performance optimizations to the workflow runner loop improve scalability (#904).
• Improve type coercion error messages for nested types (#917 #825 @​hexylena).
• Preserve CLI-subprocess backend logs from all attempts of a retried task (#921 #787 @​hexylena).
• Pinpoint the incomplete calls in the UncallableWorkflow error message (#919 #744 @​ahvigil).

Experimental WDL feature: failure-tolerant call?

In this release, WDL version development gains call?, a form of call that tolerates task execution failures. Outputs of a call? are optional to the caller (similar to how values in if workflow sections are optional outside), and become None in the event of a tolerated failure.

Typical use case: a driver workflow scattering a per-sample analysis across N samples, where for sufficiently large N, a few will end up failing for unforeseen reasons. It may still be useful to carry on the rest of the workflow and leave the failures for later follow-up.

version development
workflow batch {
input {
Array[File] bams
}
scatter (bam in bams) {
    call? analyze_sample { input: bam = bam }
    String? failed = if defined(analyze_sample.report) then None else basename(bam)
}
output {
Array[File] reports = select_all(analyze_sample.report)
Array[String] failed_samples = select_all(failed)
}

}
...

This workflow ends up with a report from every sample that succeeded, plus the names of the ones that experienced a tolerated failure. Tolerated failures include CommandFailed, DownloadFailed, and other execution problems (after retry exhaustion); but exclude WDL-level runtime errors such as output file not found, array access beyond length, division by zero, etc. A tolerated failure never goes into the call cache, so rerunning the workflow re-executes those calls.

Commits

• d081a81 alternate backend tests in manual CI workflow (#929)
• 0bfd3fa Update default task image to ubuntu:22.04 (#925)
• 1084166 clean up old conda/pythonjsonlogger workaround (#923)
• 531a228 tools_image: bump base image to ubuntu:22.04 (jammy) (#924)
• 4a3be55 delete obsolete PR template (#928)
• c69ec12 bump docker dependencies (#926)
• a547066 test: eliminate mtime race in test_call_try_call_cache (#927)
• 1e83351 [experimental] failure-tolerant call? (#858)
• 345898b S3 downloader: inherit region along with host_credentials (#922)
• 0172d93 advance to python3.10+ (#892)
• Additional commits viewable in compare view

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