Design Patterns for Apps and Workflows
Second Workflow
workflow_from_wdl
Importing a workflow from a WDL specification based on Docker images provides convenient way to express precisionFDA workflows in a serialized textual format. From My Home / Workflows, click the Create Workflow button, and click the Import from *.wdl file button. Enter the following WDL in the text input and click Import.
version 1.0
workflow bwa {
Int threads
Int min_seed_length
Int min_std_max_min
File reference
File reads
call bwa_mem_tool {
threads = threads,
min_seed_length = min_seed_length,
min_std_max_min = min_std_max_min,
reference = reference,
reads = reads
}
}
task bwa_mem_tool {
Int threads
Int min_seed_length
Int min_std_max_min
File reference
File reads
command {
bwa mem -t ${threads} \
-k ${min_seed_length} \
-I ${sep=',' min_std_max_min+} \
${reference} \
${sep=' ' reads+} > output.sam
}
output {
File sam = "output.sam"
}
runtime {
docker: "broadinstitute/baseimg"
}
}
Like workflows created through the web inteface, WDL-based workflows can be updated and run.
