Mike Lin

(My 2p) If we were starting WDL over again from scratch, then I'd certainly make environment variables the default...but today I think the feature has enough practical utility to introduce...

Prototyping the `env` declaration prefix: https://github.com/chanzuckerberg/miniwdl/pull/617

Included this feature in [miniwdl v1.8.0](https://github.com/chanzuckerberg/miniwdl/releases/tag/v1.8.0) `version development`; def invite anyone interested to hammer on it, can still change.

superseded by #617

Hi all, just a comment here, I'd consider generalizing/weakening this to say that the File/Directory representation may be a JSON object with a `location` key and *whatever else* the engine...

@yunhailuo "Yes" but it just [uses the first one](https://github.com/chanzuckerberg/miniwdl/blob/6dfe83781f74a8e248727eb61c31e1c7562bd26e/WDL/runtime/task_container.py#L209-L212) always. Only because we didn't get to making it do something smarter than that. Requirements input is welcome!

@lh3 I saw this too testing my [fork of fastp](https://github.com/OpenGene/fastp/compare/master...mlin:fastp:mlin/sdust?expand=1) integrating your code. I'm now just trimming the last masked range in the obvious way if it overhangs the sequence...

Here's a more-troubling case, where an entire range falls beyond the sequence length: ``` $ echo -e '>x\nATGTTTATGCTCATCGCTAAAAAGATTAAAATCGTTTGAGTTAAAGGATTTCACATGCTCGCTTTAGAAATTTATATTGATATTTGTTTGAAAGACGCTTTAATAGATTANTTCGTTTGAAAAAGGCTTTGATGATTTTTTTTATGTGGA' | tee x.fastq | wc -c 154 $ ./sdust x.fastq x 167...

Closing as superseded by #617 / https://github.com/openwdl/wdl/pull/504

To do: start allowing extra fields, but display warnings during input parsing