toil 8.1.0b1__py3-none-any.whl → 9.0.0__py3-none-any.whl

toil/test/wdl/testfiles/random.wdl

@@ -0,0 +1,66 @@
+version 1.0
+
+workflow random {
+    input {
+        Int wf_input = 1
+        Int task_1_input = 1
+        Int task_2_input = 1
+    }
+
+    call dice_task {
+    input:
+        task_input=task_1_input
+    }
+
+    call read_task {
+    input:
+        to_read=dice_task.out,
+        task_input=task_2_input
+    }
+
+    output {
+        String value_seen = read_task.read
+        String value_written = read_task.wrote
+    }
+}
+
+task dice_task {
+    input {
+        Int task_input
+    }
+
+    command <<<
+        cat /proc/sys/kernel/random/uuid
+    >>>
+
+    output {
+        File out = stdout()
+    }
+
+    runtime {
+        docker: "ubuntu:24.04"
+    }
+}
+
+task read_task {
+    input {
+        File to_read
+        Int task_input
+    }
+
+    String value_read = read_lines(to_read)[0]
+
+    command <<<
+        echo "~{value_read} $(cat /proc/sys/kernel/random/uuid)"
+    >>>
+
+    output {
+        String read = value_read
+        String wrote = read_lines(stdout())[0]
+    }
+
+    runtime {
+        docker: "ubuntu:24.04"
+    }
+}
+

toil/test/wdl/testfiles/read_file.wdl

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+version 1.0
+
+# Workflow to read a file from a string path
+
+workflow read_file {
+
+    input {
+        String input_string
+    }
+
+    Array[String] the_lines = read_lines(input_string)
+
+    output {
+        Array[String] lines = the_lines
+        File remade_file = write_lines(the_lines)
+    }
+
+}

toil/test/wdl/testfiles/string_file_coercion.json

@@ -0,0 +1 @@
+{"StringFileCoercion.opt_file": "empty.txt"}

toil/test/wdl/testfiles/string_file_coercion.wdl

@@ -0,0 +1,35 @@
+version 1.0
+
+workflow StringFileCoercion {
+
+    input {
+        File? opt_file
+    }
+
+    if (defined(opt_file)) {
+        call UseFile {
+            input:
+                # Exciting trick from https://github.com/broadinstitute/GATK-for-Microbes/blob/51f60135abd3f61efd0dcbe1e87c9aa89f5fb91c/wdl/shortReads/MicrobialGenomePipeline.wdl#L79C35-L79C44
+                input_file = select_first([opt_file, ""])
+        }
+    }
+
+    output {
+        File? output_file = UseFile.output_file
+    }
+}
+
+
+task UseFile {
+    input {
+        File input_file
+    }
+
+    command <<<
+        cat ~{input_file} | wc -c > output.txt
+    >>>
+
+    output {
+        File output_file = "output.txt"
+    }
+}

toil/test/wdl/testfiles/test.json

@@ -0,0 +1,4 @@
+{
+  "key1": "value1",
+  "key2": "value2"
+}

toil/test/wdl/testfiles/test_boolean.txt

@@ -0,0 +1 @@
+true

toil/test/wdl/testfiles/test_float.txt

@@ -0,0 +1 @@
+11.2345

toil/test/wdl/testfiles/test_int.txt

@@ -0,0 +1 @@
+11

toil/test/wdl/testfiles/test_lines.txt

@@ -0,0 +1,5 @@
+line 1
+		line 2 with tabs
+ line 3
+
+line 5

toil/test/wdl/testfiles/test_map.txt

@@ -0,0 +1,2 @@
+key1	value1
+key2	value2

toil/test/wdl/testfiles/test_string.txt

@@ -0,0 +1 @@
+A Whale of a Tale.

toil/test/wdl/testfiles/url_to_file.wdl

@@ -0,0 +1,13 @@
+version 1.0
+
+workflow url_to_file {
+    input {
+    }
+
+    File the_file = "https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chrom.sizes"
+
+    output {
+        File out_file = the_file
+        String first_line = read_lines(the_file)[0]
+    }
+}

toil/test/wdl/testfiles/url_to_optional_file.wdl

@@ -0,0 +1,14 @@
+version 1.0
+
+workflow url_to_optional_file {
+    input {
+        Int http_code = 404
+        String base_url = "https://httpstat.us/"
+    }
+    
+    File? the_file = base_url + http_code
+
+    output {
+        File? out_file = the_file
+    }
+}

toil/test/wdl/testfiles/vocab.json

@@ -0,0 +1 @@
+{}

toil/test/wdl/testfiles/vocab.wdl

@@ -0,0 +1,66 @@
+workflow vocabulary {
+
+  #####################################################################
+  # $primitive_type = ('Boolean' | 'Int' | 'Float' | 'File' | 'String')
+  Boolean bool1
+  Int int1
+  Float float1
+  File file1
+  String string1
+
+  Boolean bool2 = true
+  Int int2 = 1
+  Float float2 = 1.1
+  File file2 = 'src/toil/test/wdl/test.tsv'
+  String string2 = 'x'
+
+  Boolean bool3 = true
+  Int int3 = 1
+  Float float3 = 1.1
+  File file3 = 'src/toil/test/wdl/test.csv'
+  String string3 = 'x'
+
+  #####################################################################
+  # $array_type = 'Array' '[' ($primitive_type | $object_type | $array_type) ']'
+  Array[Boolean] arraybool1
+  Array[Int] arrayint1
+  Array[Float] arrayfloat1
+  Array[File] arrayfile1
+  Array[String] arraystring1
+
+  Array[Array[Boolean]] arrayarraybool1
+  Array[Array[Int]] arrayarrayint1
+  Array[Array[Float]] arrayarrayfloat1
+  Array[Array[File]] arrayarrayfile1
+  Array[Array[String]] arrayarraystring1
+
+  #####################################################################
+  # $type_postfix_quantifier = '?' | '+'
+  String joinedstring = string2 + string3 + "x"
+  Int joinedint = int2 + int3 + 1
+  Float joinedfloat = float2 + float3 + 1.1
+
+  Boolean? boolo1
+  Int? into1
+  Float? floato1
+  File? fileo1
+  String? stringo1
+
+  Boolean? boolo2 = true
+  Int? into2 = 1
+  Float? floato2 = 1.1
+  File? fileo2 = 'src/toil/test/wdl/test.csv'
+  String? stringo2 = 'x'
+
+  #####################################################################
+  # $object_type = 'Object'
+  # $map_type = 'Map' '[' $primitive_type ',' ($primitive_type | $array_type | $map_type | $object_type) ']'
+  # currently unsupported
+
+  #####################################################################
+  # demonstrate function usage
+  Int additional_disk = select_first([into1, 20])
+  Int num_of_bqsr_scatters = length([1,1,1,1])
+  Int bqsr_divisor = if int3 > 1 then additional_disk else 1
+  Float disk_size = (floato2 / bqsr_divisor) + additional_disk
+}

toil/test/wdl/testfiles/wait.wdl

@@ -0,0 +1,34 @@
+version 1.0
+
+workflow wait {
+    input {
+    }
+
+    call waiter_task {
+    input:
+    }
+
+    output {
+        String result = read_lines(waiter_task.out)[0]
+    }
+}
+
+task waiter_task {
+    input {
+    }
+
+    command <<<
+        sleep 10 &
+        sleep 2 &
+        wait
+        echo "waited"
+    >>>
+
+    output {
+        File out = stdout()
+    }
+
+    runtime {
+        docker: "ubuntu:22.04"
+    }
+}

toil/test/wdl/wdl_specification/type_pair.json

@@ -0,0 +1,23 @@
+{
+  "typePairWorkflow.test_pair": {
+    "left": 23,
+    "right": "twenty-three"
+  },
+  "typePairWorkflow.test_pair_pair": {
+    "left": "a",
+    "right": {
+      "left": "a.bam",
+      "right": "a.bai"
+    }
+  },
+  "typePairWorkflow.test_pair_file": {
+    "left": "whale",
+    "right": "src/toil/test/wdl/testfiles/test_string.txt"
+  },
+  "typePairWorkflow.test_array_pair_file": [
+    {
+      "left": "test_A",
+      "right": "src/toil/test/wdl/testfiles/test_boolean.txt"
+    }
+  ]
+}

toil/test/wdl/wdl_specification/type_pair_basic.wdl

@@ -0,0 +1,36 @@
+workflow typePairWorkflow {
+  # test conformance with the WDL language specification - Pair Literals
+
+  Pair[Int, String] test_pair
+
+  # a pair inside a pair
+  Pair[String, Pair[String, String]] test_pair_pair
+
+  # a pair defined inside WDL
+  Pair[Int, String] test_pair_from_wdl = (23, "twenty-three")
+
+  call copy_output {
+    input:
+      test_pair=test_pair,
+      test_pair_pair=test_pair_pair,
+      test_pair_from_wdl=test_pair_from_wdl
+  }
+}
+
+task copy_output {
+  Pair[Int, String] test_pair
+  Pair[String, Pair[String, String]] test_pair_pair
+  Pair[Int, String] test_pair_from_wdl
+
+  command {
+    cp ${write_json([
+                    test_pair.left,
+                    test_pair.right,
+                    test_pair_pair.right.right,
+                    test_pair_from_wdl])} output.txt
+  }
+
+ output {
+    File the_output = 'output.txt'
+ }
+}

toil/test/wdl/wdl_specification/type_pair_with_files.wdl

@@ -0,0 +1,36 @@
+workflow typePairWorkflow {
+  # test conformance with the WDL language specification - Pair Literals
+
+  # file import
+  Pair[String, File] test_pair_file
+
+  # file import with arrays
+  Array[Pair[String, File]] test_array_pair_file
+
+  call copy_output {
+    input:
+      test_pair_file=test_pair_file,
+      test_array_pair_file=test_array_pair_file
+  }
+}
+
+task copy_output {
+  Pair[String, File] test_pair_file
+  Array[Pair[String, File]] test_array_pair_file
+
+  # pairs defined in WDL in task
+  Array[Pair[String, File]] test_array_pair_file_from_wdl_in_task = [
+    ('test_A', 'src/toil/test/wdl/testfiles/test_int.txt'),
+    ('test_B', 'src/toil/test/wdl/testfiles/test_string.txt')]
+
+  command {
+    cp ${write_json([
+                    read_lines(test_pair_file.right),
+                    read_lines(select_first(test_array_pair_file).right),
+                    read_lines(select_first(test_array_pair_file_from_wdl_in_task).right)])} output.txt
+  }
+
+ output {
+    File the_output = 'output.txt'
+ }
+}

toil/test/wdl/wdl_specification/v1_spec.json

@@ -0,0 +1 @@
+{}

toil/test/wdl/wdl_specification/v1_spec_declaration.wdl

@@ -0,0 +1,39 @@
+
+# Basic declaration example modified from the WDL 1.0 spec:
+# https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#declarations
+
+version 1.0
+
+task test {
+  input {
+    String var
+  }
+  command <<<
+    echo "Hello, ~{var}!"
+  >>>
+
+  output {
+    String value = read_string(stdout())
+  }
+}
+
+task test2 {
+  input {
+    Array[String] array
+  }
+
+  command <<<
+    echo "~{sep='; ' array}" > output.txt
+  >>>
+
+  output {
+    File the_output = 'output.txt'
+  }
+}
+
+workflow wf {
+  call test as x {input: var="x"}
+  call test as y {input: var="y"}
+  Array[String] strs = [x.value, y.value]
+  call test2 as z {input: array=strs}
+}