Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

json array problem

xiuczxiucz Member

Hi,
I am trying to use wdl to scatter my BQSR step, but it reported an error:

[2019-05-09 15:07:48,46] [error] WorkflowManagerActor Workflow 4c1519dc-b82f-459c-a7db-2b3faf3a77e7 failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
Failed to evaluate input 'known_indels_sites_VCFs' (reason 1 of 1): No coercion defined from '["~/database/hg19/gatk_bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf","~/database/hg19/gatk_bundle/1000G_phase1.indels.hg19.sites.vcf"]' of type 'spray.json.JsArray' to 'File'.
Failed to evaluate input 'known_indels_sites_indices' (reason 1 of 1): No coercion defined from '["~/database/hg19/gatk_bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx","~/database/hg19/gatk_bundle/1000G_phase1.indels.hg19.sites.vcf.idx"]' of type 'spray.json.JsArray' to 'File'.

my json file for this part:

"wesbqsr.known_indels_sites_VCFs": [
    "~/database/hg19/gatk_bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf",
    "~/database/hg19/gatk_bundle/1000G_phase1.indels.hg19.sites.vcf"
  ],
  "wesbqsr.output_bam_basename": "NA12878",
  "wesbqsr.known_indels_sites_indices": [
  "~/database/hg19/gatk_bundle/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx",
  "~/database/hg19/gatk_bundle/1000G_phase1.indels.hg19.sites.vcf.idx"
  ],
  "wesbqsr.base_file_name": "NA12878",

Can you give me some suggestions , thanks a lot.

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