dxCompiler takes a pipeline written in the Workflow Description Language (WDL) or Common Workflow Language and compiles it to an equivalent workflow on the DNAnexus platform. WDL draft-2 and versions 1.0 and 1.1 are fully supported. Support for WDL 2.0 (aka 'development') and CWL 1.2 are under active development and not yet production-ready.

Prerequisites:

• DNAnexus platform account
• dx-toolkit
• java 8+
• python 3.x
• docker if you want to invoke dxCompiler with the run-dxcompiler-docker script using a public dnanexus/dxcompiler docker cointainer.

Make sure you've installed the dx-toolkit CLI, and initialized it with dx login. Download the latest compiler jar file from the releases page.

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 comprise 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/ucsc_cgl/samtools"
    }
    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/ucsc_cgl/samtools"
    }
    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 several platform objects.

• A workflow bam_chrom_counter
• Two applets that can be called independently: slice_bam, and count_bam
• A few auxiliary applets that process workflow inputs, outputs, and launch the scatter.

These objects are all created in the specified DNAnexus project and folder. The generated workflow can be run using dx run. For example:

dx run bam_chrom_counter -istage-common.bam=project-xxxx:file-yyyy

The compiled workflow can be executed via the DNAnexus command line client or web UI:

dxCompiler uses wdlTools, a parser that adheres strictly to the WDL specifications. Most of the problematic automatic type conversions that are allowed by some other WDL runtime engines are not allowed by dxCompiler. Please use the command line tools in wdlTools (e.g. check and lint) to validate your WDL files before trying to compile them with dxCompiler.

• 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.wdl imports B.wdl and A.wdl defines workflow foo, then B.wdl could not have a workflow or task named foo
  • The Directory type is only supported in stand-alone tasks, not yet in workflows
• WDL only
  • Workflows with forward references (i.e. a variable referenced before it is declared) are not yet supported.
  • The alternative workflow output syntax that has been deprecated since WDL draft2 is not supported
• CWL only
  • Nested workflows (i.e. a workflow step calling another workflow) are not yet supported
  • In-line processes in workflow steps must have explicit IDs

• Advanced options explains additional compiler options
• Internals describes current compiler structure (work in progress)
• Tips examples for how to write good WDL code
• A high-level list of changes between WDL draft-2 and version 1.0

See the development guide for more information on how to set up your development environment to contribute to dxCompiler and how to test your updates.

This software is a community effort! You can browse any of the contributions, that are not a part of dxCompiler main source codebase, below in our contrib folder, and add your own (see Contributing to dxCompiler).

Let us know if you would like to contribute, request a feature, or report a bug.