dxCompiler
An introduction to using dxCompiler, a tool for compiling WDL and CWL workflows on the DNAnexus Platform
dxCompiler is a tool for compiling pipelines written in the Workflow Description Language (WDL) and the Common Workflow Language (CWL) to equivalent workflows on the DNAnexus Platform.
Below we introduce a few use cases for dxCompiler. This tool can be downloaded from the dxCompiler GitHub repository, which also contains more advanced options including DNAnexus extensions and integration with private Docker repositories.
dxCompiler Setup
For information on how to set up dxCompiler, see instructions on the dxCompiler GitHub page.
WDL Example
Validating a Workflow
dxCompiler uses wdlTools, a parser that adheres strictly to the WDL specifications. Most of the problematic automatic type conversions that are allowed by other WDL runtime engines are not allowed by dxCompiler. Use the command line tools in wdlTools to validate your WDL files before trying to compile them with dxCompiler. Tools like check and lint are especially useful for this validation.
Compiling and Running a Workflow
The bam_chrom_counter workflow is written in WDL. Task slice_bam splits a BAM file into an array of sub-files. Task count_bam counts the number of alignments on a BAM file. The workflow takes an input BAM file, calls slice_bam to split it into chromosomes, and calls count_bam in parallel on each chromosome. The results form a BAM index file, and an array with the number of reads per chromosome.
version 1.0
workflow bam_chrom_counter {
input {
File bam
}
call slice_bam {
input : bam = bam
}
scatter (slice in slice_bam.slices) {
call count_bam {
input: bam = slice
}
}
output {
File bai = slice_bam.bai
Array[Int] count = count_bam.count
}
}
task slice_bam {
input {
File bam
Int num_chrom = 22
}
command <<<
set -ex
samtools index ~{bam}
mkdir slices/
for i in `seq ~{num_chrom}`; do
samtools view -b ~{bam} -o slices/$i.bam $i
done
>>>
runtime {
docker: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
}
output {
File bai = "~{bam}.bai"
Array[File] slices = glob("slices/*.bam")
}
}
task count_bam {
input {
File bam
}
command <<<
samtools view -c ~{bam}
>>>
runtime {
docker: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
}
output {
Int count = read_int(stdout())
}
}From the command line, we can compile the workflow to the DNAnexus Platform using the dxCompiler jar file.
java -jar dxCompiler.jar compile bam_chrom_counter.wdl \
-project project-xxxx -folder /my/workflows/This compiles the source WDL file to platform objects in the specified DNAnexus project project-xxxx under folder /my/workflows/
A workflow
bam_chrom_counterTwo applets that can be called independently:
slice_bam, andcount_bamA few auxiliary applets that process workflow inputs, outputs, and launch the scatter.
You can review the structure of the compiled DNAnexus workflow using the describe dxCompiler command. The output shows the generated DNAnexus workflows and applets in a tree that describes a caller/callee relationship.
$ java -jar dxCompiler.jar describe workflow-G3P0jFQ0Fgk3Z7855fqKyjPy --pretty
Workflow: bam_chrom_counter
├───App Inputs: common
├───App Task: slice_bam
├───App Fragment: scatter (slice in slice_bam.slices)
│ └───App Task: count_bam
└───App Outputs: outputsThe generated workflow can be executed from the UI or via the DNAnexus command-line client. For example, to run the workflow with the input BAM file project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGV, use the following command:
dx run bam_chrom_counter \
-istage-common.bam=project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGVAlternatively, you can also convert a Cromwell JSON format input file into a DNAnexus format when compiling the workflow. Then you can pass the DNAnexus input file to dx run using -f option as described in detail in the dxCompiler expert options documentation.
$ java -jar dxCompiler.jar compile bam_chrom_counter.wdl \
-project project-xxxx -folder /my/workflows/ \
-inputs bam_chrom_counter_input.json
$ dx run bam_chrom_counter -f bam_chrom_counter_input.dx.jsonAfter launching the workflow analysis, you can monitor workflow execution via the CLI or monitor workflow execution via the UI.
The CLI sessions show the executed workflow:
$ dx find executions -n1
* bam_chrom_counter (done) analysis-G3P0kGj0Fgk8ZY0645QYZ9bB
│ demo-user 2022-03-01 11:42:59
├── * outputs (bam_chrom_counter_outputs:main) (done) job-G3P0kkQ0Fgk8ZY0645QYZ9bX
│ demo-user 2022-03-01 11:43:44 (runtime 0:00:42)
├── * scatter (slice in slice_bam.slices) (bam_chrom_counter_frag_stage-1:main) (done) job-G3P0kj00Fgk8ZY0645QYZ9bV
│ │ demo-user 2022-03-01 11:43:38 (runtime 0:00:46)
│ ├── collect_scatter (bam_chrom_counter_frag_stage-1:collect) (done) job-G3P1Gb80Fgk8gx406ppxVZX6
│ │ demo-user 2022-03-01 12:24:05 (runtime 0:00:42)
│ ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1Gb80Fgk3ZjYx714yFZyQ
│ │ demo-user 2022-03-01 12:24:05 (runtime 0:01:31)
│ ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1Gb00FgkBb45v7197QVb2
│ │ demo-user 2022-03-01 12:24:04 (runtime 0:01:34)
...
│ ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZQ0Fgk0QBKp6pVZgzFg
│ │ demo-user 2022-03-01 12:24:01 (runtime 0:01:33)
│ ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZ80Fgk9vFj26Vg599P4
│ │ demo-user 2022-03-01 12:24:01 (runtime 0:01:33)
│ └── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZ80Fgk6VJ5v6kGYp5k9
│ demo-user 2022-03-01 12:24:01 (runtime 0:01:53)
├── * slice_bam (done) job-G3P0kfQ0Fgk8ZY0645QYZ9bQ
│ demo-user 2022-03-01 11:43:31 (runtime 0:37:14)
└── * common (bam_chrom_counter_common:main) (done) job-G3P0kZj0Fgk8ZY0645QYZ9bP
demo-user 2022-03-01 11:43:25 (runtime 0:00:45)The snapshot below shows what you will see from the UI when the workflow execution is completed:
CWL Example
Preprocessing a CWL Workflow
dxCompiler requires the source CWL file to be "packed" as a cwl.json file, which contains a single compound workflow with all the dependent processes included. You might need to upgrade the version of your workflow to CWL v1.2.
We'll use the bam_chrom_counter CWL workflow similar to the WDL example above to illustrate upgrading, packing and running a CWL workflow. This workflow is written in CWL v1.0 and the top-level Workflow in bam_chrom_counter.cwl calls the two CommandLineTool tools in slice_bam.cwl and count_bam.cwl.
cwlVersion: v1.0
id: bam_chrom_counter
class: Workflow
requirements:
- class: ScatterFeatureRequirement
inputs:
- id: bam
type: File
# upload this local file to the platform and replace the path below with the DNAnexus URI "dx://project-xxx:file-yyyy"
default: "path/to/my/input_bam"
outputs:
- id: bai
type: File
outputSource: slice_bam/bai
- id: count
type: int[]
outputSource: count_bam/count
steps:
- id: slice_bam
run: slice_bam.cwl
in:
bam: bam
out: [bai, slices]
- id: count_bam
run: count_bam.cwl
scatter: bam
in:
bam: slice_bam/slices
out: [count]cwlVersion: v1.0
id: slice_bam
class: CommandLineTool
inputs:
- id: bam
type: File
- id: num_chrom
default: 22
type: int
outputs:
- id: bai
type: File
outputBinding:
glob: $(inputs.bam.basename).bai
- id: slices
type: File[]
outputBinding:
glob: "slices/*.bam"
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
- class: InitialWorkDirRequirement
listing:
- entryname: slice_bam.sh
entry: |-
set -ex
samtools index $1
mkdir slices/
for i in `seq $2`; do
samtools view -b $1 -o slices/$i.bam $i
done
- entry: $(inputs.bam)
baseCommand: ["sh", "slice_bam.sh"]
arguments:
- position: 0
valueFrom: $(inputs.bam.basename)
- position: 1
valueFrom: $(inputs.num_chrom)
hints:
- class: NetworkAccess
networkAccess: true
- class: LoadListingRequirement
loadListing: deep_listingcwlVersion: v1.0
id: count_bam
class: CommandLineTool
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
inputs:
- id: bam
type: File
inputBinding:
position: 1
baseCommand: ["samtools", "view", "-c"]
outputs:
- id: count
type: int
outputBinding:
glob: stdout
loadContents: true
outputEval: "$(parseInt(self[0].contents))"
stdout: stdout
hints:
- class: NetworkAccess
networkAccess: true
- class: LoadListingRequirement
loadListing: deep_listingcountBefore compilation, follow the steps below to preprocess these CWL files:
De-localize all local paths referenced in the CWL: if the CWL specifies a local path, for example, a schema or a default value for a
file-type input (like the default path "path/to/my/input_bam" for inputbaminbam_chrom_counter.cwl), you need to upload this file to a DNAnexus project and then replace the local path in the CWL with its full DNAnexus URI, for example,dx://project-XXX:file-YYY.Install
cwl-upgraderand upgrade the CWL files to v1.2 (needed in this case as CWL files are in CWL v1.0):pip3 install cwl-upgrader # upgrade all dependent CWL files, which will be saved in the current working directory cd contrib/beginner_example cwl-upgrader cwl_v1.0/bam_chrom_counter.cwl cwl_v1.0/slice_bam.cwl cwl_v1.0/count_bam.cwlInstall
sbpackpackage and run thecwlpackcommand on the top-level workflow file to build a single packedbam_chrom_counter.cwl.jsonfile containing the top level workflow and all the steps it depends on:pip3 install sbpack cwlpack --add-ids --json bam_chrom_counter.cwl > bam_chrom_counter.cwl.json
Validating a Workflow
dxCompiler compiles tools/workflows written according to the CWL v1.2 standard. You can use cwltool --validate to validate the packed CWL file you want to compile.
Compiling and Running a Workflow
Once it is upgraded and packed as suggested above, we can compile it as a DNAnexus workflow and run it.
java -jar dxCompiler.jar compile bam_chrom_counter.cwl.json -project project-xxxx -folder /my/workflows/
dx run bam_chrom_counter -istage-common.bam=project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGVLimitations
WDL and CWL
Calls with missing arguments have limited support
All task and workflow names must be unique across the entire import tree
For example, if
A.wdlimportsB.wdlandA.wdldefines workflowfoo, thenB.wdlcannot have a workflow or task namedfoo
Subworkflows built from higher-level workflows are not intended to be used on their own
WDL only
Workflows with forward references are not yet supported. A forward reference is a variable referenced before it is declared.
The alternative workflow output syntax that has been deprecated since WDL draft2 is not supported
The
call ... aftersyntax introduced in WDL 1.1 is not yet supported
CWL only
Calling native DNAnexus apps/applets in CWL workflow using
dxniis not supported.SoftwareRequirementandInplaceUpdateRequirementare not yet supportedPublishing a dxCompiler-generated workflow as a global workflow is not supported
Applet and job reuse is not supported
Help String
dxCompiler's capabilities are outlined in the dxCompiler's help string below.
$ java -jar dxCompiler.jar version
2.10.1
$ java -jar dxCompiler.jar help
java -jar dxCompiler.jar <action> <parameters> [options]
Actions:
version
Prints the dxCompiler version.
config
Prints the current dxCompiler configuration.
describe <DxWorkflow ID>
Generate the JSON execution tree for a given DNAnexus workflow ID.
The workflow needs to be have been previously compiled by dxCompiler.
options
-pretty Print exec tree in "pretty" text format instead of JSON.
compile <WDL or CWL file>
Compile a WDL or CWL file to a DNAnexus workflow or applet.
options
-archive Archive older versions of applets.
-compileMode [IR, All]
Compilation mode - If not specified, the compilation
mode is "All" and the compiler will translate WDL or CWL
inputs into DNAnexus workflows and tasks.
Use "IR" if you only want to parse CWL or WDL files and
convert standard-formatted input files to DNAnexus JSON
input format without performing full compilation.
-defaults <string> JSON file with standard-formatted default values.
-defaultInstanceType <string>
The default instance type to use for "helper" applets
that perform runtime evaluation of instance type
requirements. This instance type is also used when
the '-instanceTypeSelection dynamic' option is set.
This value is overridden by any defaults set in set in the
JSON file specified by '-extras'.
-destination <string> Full platform path (project:/folder).
-execTree [json,pretty]
Print a JSON representation of the workflow.
-extras <string> JSON file with extra options (see documentation).
-inputs <string> JSON file with standard-formatted input values. May be
specified multiple times. A DNAnexus JSON input file is
generated for each standard input file.
-instanceTypeSelection [static,dynamic]
Whether to select instance types at compile time for tasks with
runtime requirements that can all be statically evaluated
(the default "static" option), or to defer instance type
selection in such cases to runtime (the "dynamic" option).
Using static instance type selection can save time, but it
requires the same set of instances to be accessible during WDL/CWL
compilation and during the runtime of the generated applets and
workflows. Use the "dynamic" option if you plan on creating global
DNAnexus workflows or cloning the generated workflows between
DNAnexus organizations with different available instance types.
-locked Create a locked workflow. When running a locked workflow,
input values may only be specified for the top-level workflow.
-leaveWorkflowsOpen Leave created workflows open (otherwise they are closed).
-p | -imports <string> Directory to search for imported WDL or CWL files. May be specified
multiple times.
-projectWideReuse Look for existing applets/workflows in the entire project
before generating new ones. The default search scope is the
target folder only.
-reorg Reorganize workflow output files.
-runtimeDebugLevel [0,1,2]
How much debug information to write to the job log at runtime.
Log the minimum (0), intermediate (1, the default), or all
debug information (2, for internal debugging).
-separateOutputs Store the output files of each call in a separate folder. The
default behavior is to put all outputs in the same folder.
-streamFiles [all,none,perfile]
Whether to mount all files with dxfuse (do not use the
download agent), to mount no files with dxfuse (only use
download agent), or to respect the per-file settings in WDL
parameter_meta sections (default).
-useManifests Use manifest files for all workflow and applet inputs and
outputs. Implies -locked.
-waitOnUpload Whether to wait for each file upload to complete.
dxni (WDL only)
DNAnexus Native call Interface. Creates stubs for calling DNAnexus executables
(apps/applets/workflows), and stores them as WDL tasks in a local file. Enables
calling existing platform executables without modification.
options:
-apps [include,exclude,only]
Option 'include' includes both apps and applets, 'exclude'
excludes apps and generates applet stubs only, 'only'
generates app stubs only.
-f | force Delete any existing output file.
-o <path> Destination file for WDL task definitions (defaults to
stdout).
-path <string> Name of a specific app or a path to a specific applet.
-r | recursive Search recursively for applets in the target folder.
Common options
-folder <string> Platform folder (defaults to '/').
-project <string> Platform project (defaults to currently selected project).
-language <string> [ver] Which language to use? May be WDL or CWL. You can optionally
specify a version. Currently: i. WDL: draft-2, 1.0, and 1.1, and
ii. CWL: 1.2 are supported and WDL development is partially
supported. The default is to auto-detect the language from the
source file.
-quiet Do not print warnings or informational outputs.
-verbose Print detailed logging.
-verboseKey <module> Print verbose output only for a specific module. May be
specified multiple times.
-logFile <path> File to use for logging output; defaults to stderr.A detailed description of the advanced dxCompiler features can be found in the public dxCompiler GitHub repository.
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