John Didion

This addresses #597. It adds an optional configuration parameter (`endpoint`) to the `download_awscli` section. If `endpoint` is specified, then it is passed as the value of the `--endpoint-url` option to...

Support alternative S3 endpoints

1

The aws cli supports alternative S3 endpoints with the `--endpoint-url` option. It would be great if miniwdl could expose some method of setting an alternative endpoint. I would be happy...

Added two new options, -Q and -L, to specify quality and length thresholds, respectively, for orphaned reads, i.e. read pairs where one mate but not both fails the initial quality...

I'd like to propose additional options for paired-end trimming that will enable different quality and length thresholds to be used to decide whether to keep a single read if one...

Let's combine what we've learned about searching for files (glob), reading in data (numpy.loadtxt), iterating over sequences (for loops), and making choices (if statements) to check all of our data...

Replace emojis with their text codes

2

This fixes linking behavior in IDEs and leaves behavior in GitHub unaffected. Note that this will break any direct links to section headings that contain emojis! ### Checklist - [x]...

### Checklist - [x] Pull request details were added to CHANGELOG.md - [x] Valid examples WDL's were added or updated to the SPEC.md (see the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) on writing markdown tests)

### Checklist - [x] Pull request details were added to CHANGELOG.md - [ ] Valid examples WDL's were added or updated to the SPEC.md (see the [guide](https://github.com/openwdl/wdl-tests/blob/main/docs/MarkdownTests.md) on writing markdown...

The general principal is to return an empty value/write an empty file when possible, and raise an error otherwise. ### Checklist - [x] Pull request details were added to CHANGELOG.md...