dxCompiler

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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
Validate the workflow
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.
Compile and run 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 comprise a bam index file, and an array with the number of reads per chromosome.
bam_chrom_counter.wdl
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version 1.0
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​
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workflow bam_chrom_counter {
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    input {
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        File bam
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    }
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​
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    call slice_bam {
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        input : bam = bam
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    }
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    scatter (slice in slice_bam.slices) {
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        call count_bam {
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            input: bam = slice
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        }
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    }
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    output {
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        File bai = slice_bam.bai
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        Array[Int] count = count_bam.count
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    }
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}
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​
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task slice_bam {
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    input {
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        File bam
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        Int num_chrom = 22
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    }
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    command <<<
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    set -ex
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    samtools index ~{bam}
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    mkdir slices/
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    for i in `seq ~{num_chrom}`; do
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        samtools view -b ~{bam} -o slices/$i.bam $i
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    done
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    >>>
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    runtime {
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        docker: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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    }
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    output {
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        File bai = "~{bam}.bai"
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        Array[File] slices = glob("slices/*.bam")
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    }
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}
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​
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task count_bam {
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    input {
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        File bam
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    }
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​
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    command <<<
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        samtools view -c ~{bam}
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    >>>
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    runtime {
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        docker: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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    }
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    output {
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        Int count = read_int(stdout())
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    }
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}bamwdl
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From the command line, we can compile the workflow to the DNAnexus platform using the dxCompiler jar file.
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$ java -jar dxCompiler.jar compile bam_chrom_counter.wdl \
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    -project project-xxxx -folder /my/workflows/
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This compiles the source WDL file to several platform objects in the specified DNAnexus project project-xxxx under folder /my/workflows/
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.
You can review the structure of the compiled DNAnexus workflow using the describe dxCompiler subcommand.  The output shows the generated DNAnexus workflows and applets in a tree that describes a caller/callee relationship.
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$ java -jar dxCompiler.jar describe workflow-G3P0jFQ0Fgk3Z7855fqKyjPy --pretty
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Workflow: bam_chrom_counter
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├───App Inputs: common
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├───App Task: slice_bam
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├───App Fragment: scatter (slice in slice_bam.slices)
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│   └───App Task: count_bam
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└───App Outputs: outputs
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The generated workflow can be executed from the web UI (see instructions here) 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:
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dx run bam_chrom_counter \
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  -istage-common.bam=project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGV
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Alternatively, 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 here.
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$ java -jar dxCompiler.jar compile bam_chrom_counter.wdl \
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   -project project-xxxx -folder /my/workflows/ \
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   -inputs bam_chrom_counter_input.json
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$ dx run bam_chrom_counter -f bam_chrom_counter_input.dx.json
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After launching the workflow analysis, you can monitor it on the CLI following these instructions or from the UI as suggested here.   CLI sessions shows the executed workflow:
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$ dx find executions -n1
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* bam_chrom_counter (done) analysis-G3P0kGj0Fgk8ZY0645QYZ9bB
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│ demo-user 2022-03-01 11:42:59
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├── * outputs (bam_chrom_counter_outputs:main) (done) job-G3P0kkQ0Fgk8ZY0645QYZ9bX
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│     demo-user 2022-03-01 11:43:44 (runtime 0:00:42)
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├── * scatter (slice in slice_bam.slices) (bam_chrom_counter_frag_stage-1:main) (done) job-G3P0kj00Fgk8ZY0645QYZ9bV
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│   │ demo-user 2022-03-01 11:43:38 (runtime 0:00:46)
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│   ├── collect_scatter (bam_chrom_counter_frag_stage-1:collect) (done) job-G3P1Gb80Fgk8gx406ppxVZX6
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│   │   demo-user 2022-03-01 12:24:05 (runtime 0:00:42)
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│   ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1Gb80Fgk3ZjYx714yFZyQ
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│   │   demo-user 2022-03-01 12:24:05 (runtime 0:01:31)
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│   ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1Gb00FgkBb45v7197QVb2
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│   │   demo-user 2022-03-01 12:24:04 (runtime 0:01:34)
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...
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│   ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZQ0Fgk0QBKp6pVZgzFg
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│   │   demo-user 2022-03-01 12:24:01 (runtime 0:01:33)
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│   ├── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZ80Fgk9vFj26Vg599P4
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│   │   demo-user 2022-03-01 12:24:01 (runtime 0:01:33)
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│   └── count_bam dx://project-FZjPqzQ0Fgk1PPxyBJq4ZP0J:file-G3P1... (count_bam:main) (done) job-G3P1GZ80Fgk6VJ5v6kGYp5k9
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│       demo-user 2022-03-01 12:24:01 (runtime 0:01:53)
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├── * slice_bam (done) job-G3P0kfQ0Fgk8ZY0645QYZ9bQ
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│     demo-user 2022-03-01 11:43:31 (runtime 0:37:14)
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└── * common (bam_chrom_counter_common:main) (done) job-G3P0kZj0Fgk8ZY0645QYZ9bP
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      demo-user 2022-03-01 11:43:25 (runtime 0:00:45)
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The snapshot below shows what you will see from the UI when the workflow execution is completed:
CWL Example
Preprocess 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. Additionally, you may 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 CommandLineTools in slice_bam.cwl and count_bam.cwl.
bam_chrom_counter.cwl
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cwlVersion: v1.0
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id: bam_chrom_counter
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class: Workflow
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requirements:
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- class: ScatterFeatureRequirement
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inputs:
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- id: bam
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  type: File
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  # upload this local file to the platform and replace the path below with the DNAnexus URI "dx://project-xxx:file-yyyy"
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  default: "path/to/my/input_bam"
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outputs:
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- id: bai
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  type: File
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  outputSource: slice_bam/bai
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- id: count
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  type: int[]
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  outputSource: count_bam/count
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steps:
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- id: slice_bam
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  run: slice_bam.cwl
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  in:
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    bam: bam
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  out: [bai, slices]
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- id: count_bam
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  run: count_bam.cwl
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  scatter: bam
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  in:
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    bam: slice_bam/slices
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  out: [count]
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slice_bam.cwl
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cwlVersion: v1.0
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id: slice_bam
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class: CommandLineTool
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inputs:
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- id: bam
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  type: File
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- id: num_chrom
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  default: 22
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  type: int
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outputs:
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- id: bai
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  type: File
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  outputBinding:
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    glob: $(inputs.bam.basename).bai
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- id: slices
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  type: File[]
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  outputBinding:
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    glob: "slices/*.bam"
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requirements:
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- class: InlineJavascriptRequirement
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- class: ShellCommandRequirement
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- class: DockerRequirement
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  dockerPull: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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- class: InitialWorkDirRequirement
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  listing:
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  - entryname: slice_bam.sh
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    entry: |-
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      set -ex
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      samtools index $1
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      mkdir slices/
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      for i in `seq $2`; do
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          samtools view -b $1 -o slices/$i.bam $i
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      done
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  - entry: $(inputs.bam)
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baseCommand: ["sh", "slice_bam.sh"]
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arguments:
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  - position: 0
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    valueFrom: $(inputs.bam.basename)
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  - position: 1
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    valueFrom: $(inputs.num_chrom)
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hints:
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- class: NetworkAccess
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  networkAccess: true
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- class: LoadListingRequirement
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  loadListing: deep_listing
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count_bam.cwl
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cwlVersion: v1.0
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id: count_bam
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class: CommandLineTool
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requirements:
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- class: InlineJavascriptRequirement
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- class: ShellCommandRequirement
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- class: DockerRequirement
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  dockerPull: "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
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inputs:
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- id: bam
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  type: File
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  inputBinding:
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    position: 1
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baseCommand: ["samtools", "view", "-c"]
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outputs:
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- id: count
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  type: int
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  outputBinding:
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    glob: stdout
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    loadContents: true
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    outputEval: "$(parseInt(self[0].contents))"
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stdout: stdout
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hints:
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- class: NetworkAccess
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  networkAccess: true
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- class: LoadListingRequirement
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  loadListing: deep_listingcount
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Before compilation, follow the steps below to preprocess these CWL files:
1.De-localize all local paths referenced in the CWL: if the CWL specifies a local path, e.g. a schema or a default value for a file-type input (like the default path "path/to/my/input_bam" for input bam in bam_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, e.g. dx://project-XXX:file-YYY.
2.Install cwl-upgrader and upgrade the CWL files to v1.2 (needed in this case as CWL files are in CWL v1.0):
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$ pip3 install cwl-upgrader
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​
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# upgrade all dependent CWL files, which will be saved in the current working directory
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$ cd contrib/beginner_example
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$ cwl-upgrader cwl_v1.0/bam_chrom_counter.cwl cwl_v1.0/slice_bam.cwl cwl_v1.0/count_bam.cwl
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3.Install sbpack package and run the cwlpack command on the top-level workflow file to build a single packed bam_chrom_counter.cwl.json file containing the top level workflow and all the steps it depends on:
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$ pip3 install sbpack
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$ cwlpack --add-ids --json bam_chrom_counter.cwl > bam_chrom_counter.cwl.json
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Validate the 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.
Compile and run workflow
Once it is upgraded and packed as suggested above, we can compile it as a DNAnexus workflow and run it.
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$ java -jar dxCompiler.jar compile bam_chrom_counter.cwl.json -project project-xxxx -folder /my/workflows/
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$ dx run bam_chrom_counter -istage-common.bam=project-BQbJpBj0bvygyQxgQ1800Jkk:file-FpQKQk00FgkGV3Vb3jJ8xqGV
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Limitations
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 cannot have a workflow or task named foo
Subworkflows built from higher-level workflows are not intented to be used on their own
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
The call ... after syntax introduced in WDL 1.1 is not yet supported
CWL only
Calling native DNAnexus apps/applets in CWL workflow using dxni is not supported.
SoftwareRequirement and InplaceUpdateRequirement are not yet supported
Publishing 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.
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$ java -jar dxCompiler.jar version
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2.10.1
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$ java -jar dxCompiler.jar help
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​
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java -jar dxCompiler.jar <action> <parameters> [options]
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​
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Actions:
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  version
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    Prints the dxCompiler version.
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​
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  config
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    Prints the current dxCompiler configuration.
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​
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  describe <DxWorkflow ID>
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    Generate the JSON execution tree for a given DNAnexus workflow ID.
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    The workflow needs to be have been previously compiled by dxCompiler.
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    options
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      -pretty                Print exec tree in "pretty" text format instead of JSON.
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​
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  compile <WDL or CWL file>
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    Compile a WDL or CWL file to a DNAnexus workflow or applet.
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    options
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      -archive               Archive older versions of applets.
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      -compileMode [IR, All]
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                             Compilation mode - If not specified, the compilation
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                             mode is "All" and the compiler will translate WDL or CWL
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                             inputs into DNAnexus workflows and tasks.
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                             Use "IR" if you only want to parse CWL or WDL files and
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                             convert standard-formatted input files to DNAnexus JSON
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                             input format without performing full compilation.
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      -defaults <string>     JSON file with standard-formatted default values.
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      -defaultInstanceType <string>
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                             The default instance type to use for "helper" applets
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                             that perform runtime evaluation of instance type
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                             requirements. This instance type is also used when
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                             the '-instanceTypeSelection dynamic' option is set.
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                             This value is overriden by any defaults set in set in the
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                             JSON file specified by '-extras'.
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      -destination <string>  Full platform path (project:/folder).
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      -execTree [json,pretty]
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                             Print a JSON representation of the workflow.
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      -extras <string>       JSON file with extra options (see documentation).
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      -inputs <string>       JSON file with standard-formatted input values. May be
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                             specified multiple times. A DNAnexus JSON input file is
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                             generated for each standard input file.
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      -instanceTypeSelection [static,dynamic]
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                             Whether to select instance types at compile time for tasks with
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                             runtime requirements that can all be statically evaluated
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                             (the default "static" option), or to defer instance type
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                             selection in such cases to runtime (the "dynamic" option).
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                             Using static instance type selection can save time, but it
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                             requires the same set of instances to be accessible during WDL/CWL
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                             compilation and during the runtime of the generated applets and
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                             workflows. Use the "dynamic" option if you plan on creating global
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                             DNAnexus workflows or cloning the generated workflows between
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                             DNAnexus organizations with different available instance types.
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      -locked                Create a locked workflow. When running a locked workflow,
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                             input values may only be specified for the top-level workflow.
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      -leaveWorkflowsOpen    Leave created workflows open (otherwise they are closed).
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      -p | -imports <string> Directory to search for imported WDL or CWL files. May be specified
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                             multiple times.
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      -projectWideReuse      Look for existing applets/workflows in the entire project
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                             before generating new ones. The default search scope is the
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                             target folder only.
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      -reorg                 Reorganize workflow output files.
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      -runtimeDebugLevel [0,1,2]
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                             How much debug information to write to the job log at runtime.
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                             Log the minimum (0), intermediate (1, the default), or all
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                             debug information (2, for internal debugging).
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      -separateOutputs       Store the output files of each call in a separate folder. The
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                             default behavior is to put all outputs in the same folder.
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      -streamFiles [all,none,perfile]
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                             Whether to mount all files with dxfuse (do not use the
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                             download agent), to mount no files with dxfuse (only use
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                             download agent), or to respect the per-file settings in WDL
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                             parameter_meta sections (default).
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      -useManifests          Use manifest files for all workflow and applet inputs and
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                             outputs. Implies -locked.
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      -waitOnUpload          Whether to wait for each file upload to complete.
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​
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  dxni (WDL only)
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    DNAnexus Native call Interface. Creates stubs for calling DNAnexus executables
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    (apps/applets/workflows), and stores them as WDL tasks in a local file. Enables
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    calling existing platform executables without modification.
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    options:
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      -apps [include,exclude,only]
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                             Option 'include' includes both apps and applets, 'exclude'
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                             excludes apps and generates applet stubs only, 'only'
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                             generates app stubs only.
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      -f | force             Delete any existing output file.
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      -o <path>              Destination file for WDL task definitions (defaults to
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                             stdout).
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      -path <string>         Name of a specific app or a path to a specific applet.
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      -r | recursive         Search recursively for applets in the target folder.
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​
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Common options
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    -folder <string>         Platform folder (defaults to '/').
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    -project <string>        Platform project (defaults to currently selected project).
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    -language <string> [ver] Which language to use? May be WDL or CWL. You can optionally
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                             specify a version. Currently: i. WDL: draft-2, 1.0, and 1.1, and
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                             ii. CWL: 1.2 are supported and WDL development is partially
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                             supported. The default is to auto-detect the language from the
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                             source file.
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    -quiet                   Do not print warnings or informational outputs.
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    -verbose                 Print detailed logging.
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    -verboseKey <module>     Print verbose output only for a specific module. May be
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                             specified multiple times.
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    -logFile <path>          File to use for logging output; defaults to stderr.
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[0m
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A detailed description of the advanced dxCompiler features can be found in the public dxCompiler github repository here.
Developing Portable Pipelines
Interactive Workstations
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Contents
dxCompiler Setup
WDL Example
CWL Example
Preprocess CWL workflow
Limitations
Help String