Parser bug when upgrading from draft-2 to v1.1

[mihirsamdarshi]

Hi, this tool is great, and I appreciate the work that's gone into this, but I'm running into an issue when I use the wdlTools upgrade feature. I was wondering what I could do to help resolve this?

I suspect that the issue has to do with the parser looking for a version regardless of whether the document is draft-2 or not

Thanks so much for this excellent tool!

I ran the command like this:

java -jar ../wdlTools-0.17.4.jar upgrade -f -s draft-2 -d 1.1 -o -O test_overwrite FastQC/fastqc.wdl

I'm on macOS Monterey 12.0.1 (x86_64) Java:

openjdk 11.0.12 2021-07-20 LTS
OpenJDK Runtime Environment Zulu11.50+19-CA (build 11.0.12+7-LTS)
OpenJDK 64-Bit Server VM Zulu11.50+19-CA (build 11.0.12+7-LTS, mixed mode)

The error that I'm getting looks like this

Upgrading FastQC/fastqc.wdl
[error] Command scallop failed
java.lang.Exception: Failed to parse FastQC/fastqc.wdl; this is likely due to a bug in the WDL code generator - please report this issue
        at wdlTools.cli.Upgrade.parseAndCheck(Upgrade.scala:23)
        at wdlTools.cli.Upgrade.apply(Upgrade.scala:52)
        at wdlTools.cli.Main$.runCommand(Main.scala:36)
        at wdlTools.cli.Main$.delayedEndpoint$wdlTools$cli$Main$1(Main.scala:48)
        at wdlTools.cli.Main$delayedInit$body.apply(Main.scala:12)
        at scala.Function0.apply$mcV$sp(Function0.scala:39)
        at scala.Function0.apply$mcV$sp$(Function0.scala:39)
        at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
        at scala.App.$anonfun$main$1(App.scala:73)
        at scala.App.$anonfun$main$1$adapted(App.scala:73)
        at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:553)
        at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:551)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:920)
        at scala.App.main(App.scala:73)
        at scala.App.main$(App.scala:71)
        at wdlTools.cli.Main$.main(Main.scala:12)
        at wdlTools.cli.Main.main(Main.scala)
Caused by: wdlTools.syntax.SyntaxException: error parsing document FastQC/fastqc.wdl
        at wdlTools.syntax.v1_1.ParseAll.parseDocument(ParseAll.scala:402)
        at wdlTools.cli.Upgrade.parseAndCheck(Upgrade.scala:20)
        ... 16 more
Caused by: java.lang.Exception: unrecognized version
        at wdlTools.syntax.v1_1.ParseTop.visitVersion(ParseTop.scala:1376)
        at wdlTools.syntax.v1_1.ParseTop.visitDocument(ParseTop.scala:1388)
        at wdlTools.syntax.v1_1.ParseTop.$anonfun$parseDocument$1(ParseTop.scala:1420)
        at wdlTools.syntax.Antlr4Util$Grammar.visitDocument(Antlr4Util.scala:255)
        at wdlTools.syntax.v1_1.ParseTop.parseDocument(ParseTop.scala:1420)
        at wdlTools.syntax.v1_1.ParseAll.parseDocument(ParseAll.scala:399)
        ... 17 more

My WDL looks like this:

task fastQC {
    File fastqr1
    File fastqr2
    String outdir
    Int memory
    Int disk_space
    Int num_threads
    Int num_preempt
    String docker

    command {
        mkdir -p ${outdir}
        fastqc -o ${outdir} ${fastqr1}
        fastqc -o ${outdir} ${fastqr2}

        tar -cvzf ${outdir}.tar.gz ./${outdir}
    }
    output {
        File fastQC_report = '${outdir}.tar.gz'
    }
    runtime {
        docker: "${docker}"
        memory: "${memory}GB"
        disks: "local-disk ${disk_space} HDD"
        cpu: "${num_threads}"
        preemptible: "${num_preempt}"
    }
}