Introduction
这里的workflow叫做helloHaplotypeCaller
;包含一个单任务即是GATK’s HaplotypeCaller。这个task输入一个file inputBAM
,输入一个file rawVCF
。
- Workflow
在workflow里,我们会执行task并指定task的执行顺序。
workflow helloHaplotypeCaller {
call haplotypeCaller
}
- Task
例子,比如像GATK RefFasta, sampleName, inputBAM是核心输入。同时GATK会自动寻找支持文件如an index & dictionary for the reference, and an index for the bam:
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"
}