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    David Heiman
    @dheiman
    @cjllanwarne that's really good to know, so in @rasmuse's suggestion, scatter is really a (possibly asynchronous) for loop?
    Chris Llanwarne
    @cjllanwarne
    for an appropriate definition of "for loop"... it evaluates all of the declarations in parallel and then "gather"s the results into the final value which would be available outside the scatter
    Jeff Gentry
    @geoffjentry
    @dheiman be careful there, you’re talking about Cromwell, not WDL
    David Heiman
    @dheiman
    @geoffjentry I did mention PAPI implementation, but yes you're right, I meant Cromwell. When I said "PAPI implementation", I should have been clearer and said "Cromwell's Google PAPI implementation." For an end-user worrying about cloud costs, implementation sometimes needs to be taken into consideration, even if it's not the "pure" thing to do in this forum. A more naive implementation of scatter could certainly always spin-up VMs.
    Peter van 't Hof
    @ffinfo
    is there an easy way to transform a Array[Struct] to Array[Struct.member] inside a task? Or is this planned?
    outside a task this can be done with a scatter, still a bit to verbose, but inside a task this is not possible.
    Peter van 't Hof
    @ffinfo
    so what would be nice if there is a map function, so like this: Array[String] bla = arrayStruct.map(_.member) for example
    or even more simple: Array[String] bla = arrayStruct.member (maybe to simple)
    Evan Benn
    @EvanTheB
    Hello, Is there any CI currently set up on the openwdl git? I would like to propose that the MD contents page at least be autogenerated, maybe by this: https://github.com/ekalinin/github-markdown-toc
    Other possibility, spellcheck
    Jeff Gentry
    @geoffjentry
    There is not. I’m happy to wire in travis or whatever to the repo if someone else (yourself?) were willing to wire in the actual tests
    Evan Benn
    @EvanTheB
    I'll have a look tonight
    Evan Benn
    @EvanTheB
    Jeff Gentry
    @geoffjentry
    @EvanTheB Cool. It looks like I already had Travis enabled so all we should need is a PR w/ an appropriate travis yaml
    Jeff Gentry
    @geoffjentry

    The following are open for voting. Votes shall be tallied on the 28th.

    Remove object from the language: openwdl/wdl#228
    Normalizing on POSIX ERE for regex: openwdl/wdl#243
    WDL is not UTF-8 encoded (note, not title of PR, but the most prominent change): openwdl/wdl#247

    There were three issues which recently passed voting and are waiting on implementation:

    Clarifying type conversions & meanings: openwdl/wdl#235
    Updating version statement: openwdl/wdl#245
    Adding keys function: openwdl/wdl#244

    Also I'd like to draw attention again to the Directory proposal, please do comment if you have anything to say as it's coming close to voting: openwdl/wdl#241

    That’s “now UTF-8 encoded”, not “not UTF-8"
    Jeff Gentry
    @geoffjentry

    It's been a long time in coming, but the WDL Directory type PR is now open for voting. Votes will be accumulated over the next 10 days, please mark either +1 or -1 to show support (or lack thereof).

    Feel free to make comments, but please note that you are voting on the PR as is. Comments can be taken as suggestions for future work or to explain why you're -1.

    openwdl/wdl#241

    Anton Kulaga
    @antonkulaga
    Finally!
    Jeff Gentry
    @geoffjentry
    @antonkulaga There’s already a Cromwell PR which will merge in quickly if this OpenWDL PR passes, so your prayers might finally be answered :)
    Anton Kulaga
    @antonkulaga
    Wonderful! I see only positive votes in the comments to the PR
    Jeff Gentry
    @geoffjentry

    Just a note that the proposed spec change for Directory type has passed and is waiting an implementation. There's a Cromwell PR which implements this, it may or may not need a bit of refinement following the latest Directory discussions, but either way that should move quickly. I know there are many people who have been waiting patiently for this!

    There's also a new spec change request: "Add 'None' to spec" openwdl/wdl#263

    This proposes a "None" value for optional fields.

    Please comment as you see fit

    Jeff Gentry
    @geoffjentry

    There's a PR open for voting:

    "Add None to spec": openwdl/wdl#263

    There were also two PRs which opened up recently. I'll give them about a week to garner commentary before bringing to a vote:

    Clarifying how comments work: openwdl/wdl#277
    Struct literals: openwdl/wdl#278

    Morgan Taschuk
    @morgantaschuk
    hi all! Can someone tell me how to get on the mailing list for OpenWDL? When I follow the link on the website it tells me only "You do not have permission to access this content. (#418)
    "
    Jeff Gentry
    @geoffjentry
    Hmm, let me take a look
    oh bleh. a while back google fiddled with group settings. i’ve run into this a few times w/ broad GGs as well
    will fix
    Morgan Taschuk
    @morgantaschuk
    Thanks
    Jeff Gentry
    @geoffjentry
    @morgantaschuk try it now?
    Morgan Taschuk
    @morgantaschuk
    Success!
    Jeff Gentry
    @geoffjentry
    took me a few tries, go figure - reading the helpful FAQ google put at the top of the new settings was waht i needed :)
    Morgan Taschuk
    @morgantaschuk
    Nice! Now I have to convince Google groups to accept my OICR email.
    Jeff Gentry
    @geoffjentry
    That I probably can’t help out with :’(
    Morgan Taschuk
    @morgantaschuk
    I think I did it!
    Jeff Gentry
    @geoffjentry
    Sweet!
    Matthew Pocock
    @drdozer
    hey - is this a good place to find out about cromwell and wdl and writing workflows?
    @morgantaschuk hi!!
    Michael Franklin
    @illusional
    Good place to ask questions!
    Matthew Pocock
    @drdozer
    cool - I got the hello world example running first time, which is a good sign
    Matthew Pocock
    @drdozer
    is there a library of example wdls? I want to start off by blasting the sequences from a bunch of fasta files
    Michael Franklin
    @illusional

    I'm not sure, the Broad publish some of their pipelines here (their specific "Data pre-processing for variant discovery" GitHub.

    I've got a few examples of WDL tool wrappers and a workflow for alignment (Cutadapt + BWA + SortSam).

    Hopefully this gives you some basic examples!

    The docs have some good examples too.
    Matthew Pocock
    @drdozer
    thanks
    Morgan Taschuk
    @morgantaschuk
    @drdozer Hi Matt! Long time no see.
    Jeff Gentry
    @geoffjentry
    There’s a group called BioWDL who are trying to make a general WDL repository: https://github.com/biowdl
    Matthew Pocock
    @drdozer
    cheers - I'll have a rummage through that
    I may end up with a bunch of short biopython or rust scripts joined together with wdl, perhaps
    Jeff Gentry
    @geoffjentry
    @drdozer Great! If you get to a point where you want to share workflows with others, I’d recommend looking at one of the two resources I referenced above for hosting