Mike Lin

htsget referenceMD5 query parameter

1

This restores the referenceMD5 query parameter as an unambiguous way to identify the desired reference sequence in a range query, which was in the draft spec but removed in #209...

document convention for "QC squeezing" in population VCF

1

This PR documents a convention developed in [spVCF](https://github.com/mlin/spVCF) to reduce the size of population-wide VCF files (presenting the full locus x sample matrix) by selectively omitting FORMAT fields. As written,...

Setting environment variables in workflow engine container

1

miniwdl allows any of its configuration options to be overridden by environment variables ([details](https://miniwdl.readthedocs.io/en/latest/runner_reference.html?highlight=errata#configuration)). This is often a more-convenient way to tune them compared to editing a configuration file (also...

optionFileURL vs optionsFileURL in CromwellWESAdapter

3

The [docs](https://aws.github.io/amazon-genomics-cli/docs/concepts/workflows/#manifestjson-structure) and most examples use `optionFileURL` (singular) in the manifest. But [CromwellWESAdapter looks for `optionsFileURL`](https://github.com/aws/amazon-genomics-cli/blob/9f6480dcbd3bd280c822cce960aec0c6aceb7615/packages/wes_adapter/amazon_genomics/wes/adapters/CromwellWESAdapter.py#L668-L677) (plural). Also, if we [search this repo](https://github.com/aws/amazon-genomics-cli/search?q=optionsFileURL) for `optionsFileURL` (plural), there are a few...

escape sequences in regex

2

I was just battening down miniwdl's parsing of escape sequences in string literals, and got tripped up here: https://github.com/biowdl/tasks/blob/c92755e510723da731ba92637c41e58c8490b5fc/common.wdl#L219 Looking at the [WDL spec on escape sequences](https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md#whitespace-strings-identifiers-constants), do you think...

Is this a good idea? When somebody waits for this lock, it could be awhile because it's waiting on I/O.

We invoke commands with `bash -l` to create a login shell, apparently [following Cromwell](https://github.com/chanzuckerberg/miniwdl/issues/568#issuecomment-1143800205). This evaluates `/etc/profile` , `/etc/profile.d/*`, `~/.profile`, and `~/.bash_profile` which wouldn't occur in a non-login shell. In...

tighten optional-to-String coercions

1

#596 As this is a potentially-breaking change we will take some time to merge/release it, with deprecation linter warnings in the meantime (#602).

SEE: https://github.com/broadinstitute/cromwell/issues/6840 We are allowing coercion of some optional primitive types (`File?` `Directory?` `Boolean?` etc.) to non-optional `String`, but this seems indefensible when we do not allow `String?` to `String`...