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Published 20 hours ago • verified publisher icon broadinstitute

womtool fails on graph building

Open EugeneEA opened this issue 3 years ago • 1 comments

Hi I did try to build DAG for a task from WARP pipeline, and wom failed with an error https://github.com/broadinstitute/warp/issues/438 Turns out it it no a problem of a pipeline, but possibly a bug in a wom.

Best, Eugene

EugeneEA avatar Sep 20 '21 16:09 EugeneEA

The issue still persists with wom-73. It fails on /warp/tasks/broad/UnmappedBamToAlignedBam.wdl (https://github.com/broadinstitute/warp/tree/WholeGenomeReprocessing_v3.0.1) but works on other workflows from /warp/tasks/broad

olesya13 avatar Jan 14 '22 21:01 olesya13

@olesya13 it turns out that the problems are caused by lines if (unmapped_bam_size > cutoff_for_large_rg_in_gb) and unmapped_bam_size <= cutoff_for_large_rg_in_gb. If you substitute these expression to true wom will build the Dag. It seems that the wom cannot process workflow if there are such expressions which can block execution completely (if one of these two is false wfl will fail)

Best, Eugene

EugeneEA avatar Jan 29 '23 19:01 EugeneEA