Files added to dependencies
cromwell-client_1 | 2022-08-20 20:16:31.318Z info [UserActor] VALIDATING WDL at http://cromwell:8000 - (UserActor.scala:107)
cromwell-client_1 | written dependency as temp file /tmp/8610569505943648695/align_reads.wdl
cromwell-client_1 | written dependency as temp file /tmp/8610569505943648695/clean_reads.wdl
Validation output:
Failed to import 'clean_reads.wdl' (reason 1 of 1): Failed to resolve 'clean_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path
Failed to import 'align_reads.wdl' (reason 1 of 1): Failed to resolve 'align_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path
Run results in successful execution, so it is a validation issue. I wasn't able to pinpoint the root cause of the failed validation.
In https://github.com/antonkulaga/cromwell-client/blob/master/client/jvm/src/main/scala/group/research/aging/cromwell/client/CromwellClientJVMSpecific.scala
calls to produce dependencies parameter in postWorkflowStrings and validateWorkflow are identical:
zipDependencies(wdlDependencies).map(f=>ByteBuffer.wrap(f.loadBytes))
Comment says * Created by antonkulaga on 2/18/17. There is an issue with Cromwell reported sometime later: broadinstitute/cromwell#5182 might be related.
Files added to dependencies
Validation output:
Failed to import 'clean_reads.wdl' (reason 1 of 1): Failed to resolve 'clean_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path
Failed to import 'align_reads.wdl' (reason 1 of 1): Failed to resolve 'align_reads.wdl' using resolver: 'http importer (no 'relative-to' origin)' (reason 1 of 1): Relative path
Run results in successful execution, so it is a validation issue. I wasn't able to pinpoint the root cause of the failed validation.
In https://github.com/antonkulaga/cromwell-client/blob/master/client/jvm/src/main/scala/group/research/aging/cromwell/client/CromwellClientJVMSpecific.scala
calls to produce dependencies parameter in postWorkflowStrings and validateWorkflow are identical:
zipDependencies(wdlDependencies).map(f=>ByteBuffer.wrap(f.loadBytes))Comment says * Created by antonkulaga on 2/18/17. There is an issue with Cromwell reported sometime later: broadinstitute/cromwell#5182 might be related.