Hi I've just run a clone of the Somatic-SNVs-Indels-GATK4 workspace, looking over the output of the WDL in the Monitor section Mutect2.sub_bamout_size has been flagged as failed with Started: reading Pending... the actual error appears to be message: Evaluating size(M2.output_bamOut, "GB") failed: Remote host closed connection during handshake. Is there a way of getting the bamOut working as obviously these files are very handy with respect to inspecting called variants. I understand M2 is sharded across multiple instances will the normal workflow collate the multiple bamOut outputs in to a per sample BAM?
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Mutect2 workflow bam out fails
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