Fix.md

Fix

The fix command attempts to automatically fix WDL files with the following specification incompatibilities:

• String/non-String concatenations are re-written as string interpolations, .e.g.

  runtime {
    disks: "local-disk " + disk_size_gb + " SSD"
  }

  becomes

  runtime {
    disks: "local-disk ${disk_size_gb} SSD"
  }

• Declarations with type mismatches, e.g.

  String x = ceil(size(myfile))

  becomes

  Int x = ceil(size(myfile))

Additional fixes will be added as needed. Please request them by opening an issue.

Issues that cannot be fixed (partial list)

• Re-usage of variable names within the same scope, e.g.

  task bad_juju {
    input {
      String foo
    }
    ...
    output {
      Int foo
    }
  }

• Coercions from String to non-String values are allowed within the context of read_* return values, but not otherwise. For example, this is legal:

  task ok {
    command <<<
    echo "1\n2\n3" > ints.txt
    >>>
    output {
      Array[Int] ints = read_lines("ints.txt")
    }
  }

  but this is illegal:

  workflow not_ok {
    call ints_to_strings
    output {
      Array[Int] ints = ints_to_strings.strings
    }
  }
  task ints_to_strings {
    command <<<
    echo "1\n2\n3" > ints.txt
    >>>
    output {
      Array[String] strings = read_lines("ints.txt")
    }
  }

Example

$ java -jar target/wdlTools.jar fix -O gatk-fixed https://raw.githubusercontent.com/gatk-workflows/gatk4-genome-processing-pipeline/1.3.0/WholeGenomeGermlineSingleSample.wdl

Usage

Usage: wdlTools fix [OPTIONS] <path|uri>
Fix specification incompatibilities in WDL file and all its dependencies.

Options:

  -a, --antlr4-trace          enable trace logging of the ANTLR4 parser
  -f, --follow-imports        (Default) format imported files in addition to the
                              main file
      --nofollow-imports      only format the main file
  -l, --local-dir  <arg>...   directory in which to search for imports; ignored
                              if --nofollow-imports is specified
  -O, --output-dir  <arg>     Directory in which to output fixed WDL files;
                              defaults to current directory
  -o, --overwrite             Overwrite existing files
      --nooverwrite           (Default) Do not overwrite existing files
  -q, --quiet                 use less verbose output
  -s, --src-version  <arg>    WDL version of the document being upgraded
  -v, --verbose               use more verbose output
  -h, --help                  Show help message

 trailing arguments:
  uri (required)   path or String (file:// or http(s)://) to the main WDL file