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.

Single-task workflow example: helloHaplotypeCaller

KateNKateN Cambridge, MAMember, Broadie, Moderator admin
edited June 2016 in Real Workflows

For more information on this script, please read its walkthrough guide.

workflow helloHaplotypeCaller {
  call haplotypeCaller
}

#This task calls GATK's tool, HaplotypeCaller in normal mode. This tool takes a pre-processed 
#bam file and discovers variant sites. These raw variant calls are then written to a vcf file.
task haplotypeCaller {
  File GATK
  File RefFasta
  File RefIndex
  File RefDict
  String sampleName
  File inputBAM
  File bamIndex
  command {
    java -jar ${GATK} \
      -T HaplotypeCaller \
      -R ${RefFasta} \
      -I ${inputBAM} \
      -o ${sampleName}.raw.indels.snps.vcf
  }
  output {
    File rawVCF = "${sampleName}.raw.indels.snps.vcf"
  }
}
Post edited by KateN on
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