java.io.IOException: resource not found on classpath: application.conf

[mmterpstra]

Default application.json not found in classpath in precompiled jar on github (affecting multiple releases tested version 86 and 85). Tested to not be affected version 79/56. Main error below. Should be an easy fix.

Exception in thread "main" com.typesafe.config.ConfigException$IO: application: application.conf: java.io.IOException: resource not found on classpath: application.conf, application.json: java.io.IOException: resource not found on classpath: application.json, application.properties: java.io.IOException: resource not found on classpath: application.properties
        at com.typesafe.config.impl.SimpleIncluder.fromBasename(SimpleIncluder.java:236)
        at com.typesafe.config.impl.ConfigImpl.parseResourcesAnySyntax(ConfigImpl.java:133)
        at com.typesafe.config.ConfigFactory.parseResourcesAnySyntax(ConfigFactory.java:1083)
        at com.typesafe.config.impl.SimpleIncluder.includeResourceWithoutFallback(SimpleIncluder.java:123)
        at com.typesafe.config.impl.SimpleIncluder.includeResources(SimpleIncluder.java:109)
        at com.typesafe.config.impl.ConfigParser$ParseContext.parseInclude(ConfigParser.java:181)
        at com.typesafe.config.impl.ConfigParser$ParseContext.parseObject(ConfigParser.java:237)
        at com.typesafe.config.impl.ConfigParser$ParseContext.parseValue(ConfigParser.java:103)
        at com.typesafe.config.impl.ConfigParser$ParseContext.parse(ConfigParser.java:415)
        at com.typesafe.config.impl.ConfigParser.parse(ConfigParser.java:25)
        at com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:263)
        at com.typesafe.config.impl.Parseable.rawParseValue(Parseable.java:250)
        at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)
        at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)
        at com.typesafe.config.impl.Parseable.parse(Parseable.java:301)
        at com.typesafe.config.ConfigFactory.parseFile(ConfigFactory.java:793)
        at com.typesafe.config.ConfigFactory.parseApplicationReplacement(ConfigFactory.java:1166)
        at com.typesafe.config.DefaultConfigLoadingStrategy.parseApplicationConfig(DefaultConfigLoadingStrategy.java:11)
        at com.typesafe.config.ConfigFactory.defaultApplication(ConfigFactory.java:532)
        at com.typesafe.config.ConfigFactory$1.call(ConfigFactory.java:264)
        at com.typesafe.config.ConfigFactory$1.call(ConfigFactory.java:261)
        at com.typesafe.config.impl.ConfigImpl$LoaderCache.getOrElseUpdate(ConfigImpl.java:66)
        at com.typesafe.config.impl.ConfigImpl.computeCachedConfig(ConfigImpl.java:93)
        at com.typesafe.config.ConfigFactory.load(ConfigFactory.java:261)
        at com.typesafe.config.ConfigFactory.load(ConfigFactory.java:237)
        at cromwell.languages.util.ImportResolver$HttpResolver$.apply(ImportResolver.scala:237)
        at womtool.input.WomGraphMaker$.importResolvers$lzycompute$1(WomGraphMaker.scala:28)
        at womtool.input.WomGraphMaker$.importResolvers$1(WomGraphMaker.scala:27)
        at womtool.input.WomGraphMaker$.$anonfun$getBundleAndFactory$1(WomGraphMaker.scala:39)
        at scala.util.Either.flatMap(Either.scala:352)
        at womtool.input.WomGraphMaker$.getBundleAndFactory(WomGraphMaker.scala:30)
        at womtool.input.WomGraphMaker$.fromFiles(WomGraphMaker.scala:46)
        at womtool.validate.Validate$.validate(Validate.scala:26)
        at womtool.WomtoolMain$.dispatchCommand(WomtoolMain.scala:54)
        at womtool.WomtoolMain$.runWomtool(WomtoolMain.scala:161)
        at womtool.WomtoolMain$.delayedEndpoint$womtool$WomtoolMain$1(WomtoolMain.scala:166)
        at womtool.WomtoolMain$delayedInit$body.apply(WomtoolMain.scala:27)
        at scala.Function0.apply$mcV$sp(Function0.scala:42)
        at scala.Function0.apply$mcV$sp$(Function0.scala:42)
        at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17)
        at scala.App.$anonfun$main$1(App.scala:98)
        at scala.App.$anonfun$main$1$adapted(App.scala:98)
        at scala.collection.IterableOnceOps.foreach(IterableOnce.scala:575)
        at scala.collection.IterableOnceOps.foreach$(IterableOnce.scala:573)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:933)
        at scala.App.main(App.scala:98)
        at scala.App.main$(App.scala:96)
        at womtool.WomtoolMain$.main(WomtoolMain.scala:27)
        at womtool.WomtoolMain.main(WomtoolMain.scala)
Caused by: com.typesafe.config.ConfigException$IO: application.conf: java.io.IOException: resource not found on classpath: application.conf
        at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:190)
        at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:174)
        at com.typesafe.config.impl.Parseable.parse(Parseable.java:152)
        at com.typesafe.config.impl.SimpleIncluder.fromBasename(SimpleIncluder.java:185)
        ... 48 more
Caused by: java.io.IOException: resource not found on classpath: application.conf
        at com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:726)
        at com.typesafe.config.impl.Parseable$ParseableResources.rawParseValue(Parseable.java:701)
        at com.typesafe.config.impl.Parseable.parseValue(Parseable.java:180)
        ... 51 more

The backend I'm running on is slurm and local

Workflow link

https://github.com/mmterpstra/Bestie

Below are the first few lines of the config shown.

#see also https://cromwell.readthedocs.io/en/stable/backends/SLURM/
# include the application.conf at the top
include required(classpath("application"))
workflow-options {
  workflow-failure-mode = ContinueWhilePossible
  delete_intermediate_output_files = true
  final_workflow_outputs_dir = "cromwell-results",
  use_relative_output_paths = true,
  final_workflow_log_dir = "cromwell-logs",
  final_call_logs_dir = "cromwell-call_logs"
}
database {
  profile = "slick.jdbc.HsqldbProfile$"
  db {
    driver = "org.hsqldb.jdbcDriver"
    url = """
    jdbc:hsqldb:file:cromwell-executions/cromwell-db/cromwell-db;
    shutdown=false;
    hsqldb.default_table_type=cached;hsqldb.tx=mvcc;
    hsqldb.result_max_memory_rows=50000;
    hsqldb.large_data=true;
    hsqldb.applog=1;
    hsqldb.lob_compressed=true;
    hsqldb.script_format=3
    """
    connectionTimeout = 120000
    numThreads = 1
   }
}
backend {
  default = "Local"

OS and java version

Centos7 and Java/11.0.16 (openjdk)