WDLtool is now called WOMtool and lives under the Cromwell repository. Click here for WOMtool within Cromwell.
For information about how to use WOMtool, see the Cromwell documentation.
For the latest WOMtool JAR, see the Cromwell releases.
Command line utilities for interacting with WDL
The following is the toolchain used for development of wdltool. Other versions may work, but these are recommended.
sbt assembly will build a runnable JAR in target/scala-2.11/
Tests are run via sbt test. Note that the tests do require Docker to be running. To test this out while downloading the Ubuntu image that is required for tests, run docker pull ubuntu:latest prior to running sbt test
Run the JAR file with no arguments to get the usage message:
$ java -jar wdltool.jar
java -jar wdltool.jar <action> <parameters>
Actions:
validate <WDL file>
Performs full validation of the WDL file including syntax
and semantic checking
inputs <WDL file>
Write a JSON skeleton file of the inputs needed for this
workflow. Fill in the values in this JSON document and
pass it in to the 'run' subcommand.
highlight <WDL file> <html|console>
Reformats and colorizes/tags a WDL file. The second
parameter is the output type. "html" will output the WDL
file with <span> tags around elements. "console" mode
will output colorized text to the terminal
parse <WDL file>
Compares a WDL file against the grammar and writes out an
abstract syntax tree if it is valid, and a syntax error
otherwise. Note that higher-level AST checks are not done
via this sub-command and the 'validate' subcommand should
be used for full validation
Given a WDL file, this runs the full syntax checker over the file and resolves imports in the process. If any syntax errors are found, they are written out. Otherwise the program exits.
Error if a call references a task that doesn't exist:
$ java -jar wdltool.jar validate 2.wdl
ERROR: Call references a task (BADps) that doesn't exist (line 22, col 8)
call BADps
^
Error if namespace and task have the same name:
$ java -jar wdltool.jar validate 5.wdl
ERROR: Task and namespace have the same name:
Task defined here (line 3, col 6):
task ps {
^
Import statement defined here (line 1, col 20):
import "ps.wdl" as ps
^
Examine a WDL file with one workflow in it, compute all the inputs needed for that workflow and output a JSON template that the user can fill in with values. The keys in this document should remain unchanged. The values tell you what type the parameter is expecting. For example, if the value were Array[String], then it's expecting a JSON array of JSON strings, like this: ["string1", "string2", "string3"]
$ java -jar wdltool.jar inputs 3step.wdl
{
"three_step.cgrep.pattern": "String"
}
This inputs document is used as input to the run subcommand.
Formats a WDL file and semantically tags it. This takes a second parameter (html or console) which determines what the output format will be.
test.wdl
task abc {
String in
command {
echo ${in}
}
output {
String out = read_string(stdout())
}
}
workflow wf {
call abc
}
Given a WDL file input, this does grammar level syntax checks and writes out the resulting abstract syntax tree.
$ echo "workflow wf {}" | java -jar wdltool.jar parse /dev/stdin
(Document:
imports=[],
definitions=[
(Workflow:
name=<stdin:1:10 identifier "d2Y=">,
body=[]
)
]
)
This WDL file can be formatted in HTML as follows:
$ java -jar wdltool.jar highlight test.wdl html
<span class="keyword">task</span> <span class="name">abc</span> {
<span class="type">String</span> <span class="variable">in</span>
<span class="section">command</span> {
<span class="command">echo ${in}</span>
}
<span class="section">output</span> {
<span class="type">String</span> <span class="variable">out</span> = <span class="function">read_string</span>(<span class="function">stdout</span>())
}
}
<span class="keyword">workflow</span> <span class="name">wf</span> {
<span class="keyword">call</span> <span class="name">abc</span>
}
The syntax of the graph command is:
wdltool graph [--all] wdlFile.wdl
Given a WDL file input, command generates the data-flow graph through the system in .dot format.
For example the fork-join WDL:
task mkFile {
command {
for i in `seq 1 1000`
do
echo $i
done
}
output {
File numbers = stdout()
}
runtime {docker: "ubuntu:latest"}
}
task grep {
String pattern
File in_file
command {
grep '${pattern}' ${in_file} | wc -l
}
output {
Int count = read_int(stdout())
}
runtime {docker: "ubuntu:latest"}
}
task wc {
File in_file
command {
cat ${in_file} | wc -l
}
output {
Int count = read_int(stdout())
}
runtime {docker: "ubuntu:latest"}
}
task join {
Int grepCount
Int wcCount
command {
expr ${wcCount} / ${grepCount}
}
output {
Int proportion = read_int(stdout())
}
runtime {docker: "ubuntu:latest"}
}
workflow forkjoin {
call mkFile
call grep { input: in_file = mkFile.numbers }
call wc { input: in_file=mkFile.numbers }
call join { input: wcCount = wc.count, grepCount = grep.count }
output {
join.proportion
}
}
Produces the DAG:
digraph forkjoin {
"call forkjoin.mkFile" -> "call forkjoin.wc"
"call forkjoin.mkFile" -> "call forkjoin.grep"
"call forkjoin.wc" -> "call forkjoin.join"
"call forkjoin.grep" -> "call forkjoin.join"
}
If this flag is set, all WDL graph nodes become nodes in the generated DAG, even if they are not "executed". Typically this will mean task declarations and call outputs.
For example in the above example, with --all you would get:
digraph forkjoin {
"call forkjoin.grep" -> "String forkjoin.grep.pattern"
"call forkjoin.grep" -> "output { forkjoin.grep.count = read_int(stdout()) }"
"call forkjoin.grep" -> "File forkjoin.grep.in_file"
"call forkjoin.wc" -> "output { forkjoin.wc.count = read_int(stdout()) }"
"call forkjoin.grep" -> "call forkjoin.join"
"call forkjoin.wc" -> "File forkjoin.wc.in_file"
"call forkjoin.mkFile" -> "call forkjoin.grep"
"call forkjoin.join" -> "output { forkjoin.join.proportion = read_int(stdout()) }"
"call forkjoin.join" -> "Int forkjoin.join.wcCount"
"call forkjoin.wc" -> "call forkjoin.join"
"call forkjoin.mkFile" -> "output { forkjoin.mkFile.numbers = stdout() }"
"call forkjoin.mkFile" -> "call forkjoin.wc"
"call forkjoin.join" -> "Int forkjoin.join.grepCount"
}
For documentation and many examples on how to use WDL see the WDL website.