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microbiomedata / nmdc-edge

Web-based interface to the NMDC EDGE platform
https://nmdc-edge.org
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MAGs template error #243

Closed mflynn-lanl closed 1 month ago

mflynn-lanl commented 1 month ago

Workflow Name Metagenome MAGs

Project URL https://nmdc-edge.org/user/project?code=ibTDSvzItvUL5NuE

Additional Info pipeline.wdl is not being generated correctly because in the MAGs template file, in the input section for call mbin_nmdc_output.pdf_to_png as metaMAGs_vis is missing commas

Jul 11 04:12:12 edge-nmdc java[3531671]: 2024-07-11 04:12:12,264 cromwell-system-akka.dispatchers.engine-dispatcher-44 INFO  - WorkflowManagerActor: Workflow 5d3d61d2-15e0-4a7b-8a01-9b8a4c9c60dd failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
Jul 11 04:12:12 edge-nmdc java[3531671]: ERROR: Unexpected symbol (line 47, col 7) when parsing '_gen13'.
Jul 11 04:12:12 edge-nmdc java[3531671]: Expected rbrace, got container.
Jul 11 04:12:12 edge-nmdc java[3531671]:                     container = metaMAGsVis_container
Jul 11 04:12:12 edge-nmdc java[3531671]:       ^
Jul 11 04:12:12 edge-nmdc java[3531671]: $e = :identifier <=> :lparen $_gen18 :rparen -> FunctionCall( name=$0, params=$2 )
chienchi commented 1 month ago

The GTDBTK Database should be updated to use the 

  23  String <WORKFLOW>_gtdbtk_db="/refdata/GTDBTK_DB"
 String <WORKFLOW>_gtdbtk_db="/refdata/GTDBTK_DB/gtdbtk_release207_v2"