toil 8.1.0b1__py3-none-any.whl → 8.2.0__py3-none-any.whl

toil/test/wdl/lint_error.wdl

@@ -0,0 +1,9 @@
+version 1.1
+
+workflow wf {
+    input {
+      Int? foo = 42
+    }
+    output {
+    }
+}

toil/test/wdl/md5sum/empty_file.json

@@ -0,0 +1 @@
+{"ga4ghMd5.inputFile": ""}

toil/test/wdl/md5sum/md5sum-gs.json

@@ -0,0 +1 @@
+{"ga4ghMd5.inputFile": "gs://broad-public-datasets/NA12878/NA12878.cram.crai"}

toil/test/wdl/md5sum/md5sum.1.0.wdl

@@ -0,0 +1,32 @@
+version 1.0
+
+task md5 {
+  input {
+    File inputFile
+  }
+  command <<<
+    set -euf -o pipefail
+    md5sum ~{inputFile} | awk '{print $1}' > md5sum.txt
+  >>>
+
+ output {
+    File value = "md5sum.txt"
+ }
+
+ runtime {
+   docker: "ubuntu:22.04"
+   cpu: 1
+   memory: "512 MB"
+   disks: "local-disk 10 HDD"
+ }
+}
+
+workflow ga4ghMd5 {
+  input {
+    File inputFile
+  }
+  call md5 { input: inputFile=inputFile }
+  output {
+    File value = md5.value
+  }
+}

toil/test/wdl/md5sum/md5sum.input

@@ -0,0 +1 @@
+this is the test file that will be used when calculating an md5sum

toil/test/wdl/md5sum/md5sum.json

@@ -0,0 +1 @@
+{"ga4ghMd5.inputFile": "src/toil/test/wdl/md5sum/md5sum.input"}

toil/test/wdl/md5sum/md5sum.wdl

@@ -0,0 +1,25 @@
+# Note that this is a draft-WDL file; we don't have input sections, or output
+# sections on the workflow.
+task md5 {
+  File inputFile
+
+  command {
+    /bin/my_md5sum ${inputFile}
+  }
+
+ output {
+    File value = "md5sum.txt"
+ }
+
+ runtime {
+   docker: "quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4"
+   cpu: 1
+   memory: "512 MB"
+   disks: "local-disk 10 HDD"
+ }
+}
+
+workflow ga4ghMd5 {
+ File inputFile
+ call md5 { input: inputFile=inputFile }
+}

toil/test/wdl/miniwdl_self_test/inputs-namespaced.json

@@ -0,0 +1 @@
+{"hello_caller.who": "https://raw.githubusercontent.com/chanzuckerberg/miniwdl/main/tests/alyssa_ben.txt"}

toil/test/wdl/miniwdl_self_test/inputs.json

@@ -0,0 +1 @@
+{"who": "https://raw.githubusercontent.com/chanzuckerberg/miniwdl/main/tests/alyssa_ben.txt"}

toil/test/wdl/miniwdl_self_test/self_test.wdl

@@ -0,0 +1,40 @@
+# MiniWDL self-test workflow from https://github.com/chanzuckerberg/miniwdl/blob/ec4cceeb0cd277d2b4633a7fa81a9593c139e2dd/WDL/CLI.py#L1364
+version 1.0
+workflow hello_caller {
+    input {
+        File who
+    }
+    scatter (name in read_lines(who)) {
+        call hello {
+            input:
+                who = write_lines([name])
+        }
+        if (defined(hello.message)) {
+            String msg = read_string(select_first([hello.message]))
+        }
+    }
+    output {
+        Array[String] messages = select_all(msg)
+        Array[File] message_files = select_all(hello.message)
+    }
+}
+task hello {
+    input {
+        File who
+    }
+    command {
+        set -x
+        if grep -qv ^\# "${who}" ; then
+            name="$(cat ${who})"
+            mkdir messages
+            echo "Hello, $name!" | tee "messages/$name.txt" 1>&2
+        fi
+    }
+    output {
+        File? message = select_first(flatten([glob("messages/*.txt"), ["nonexistent"]]))
+    }
+    runtime {
+        docker: "ubuntu:18.04"
+        memory: "1G"
+    }
+}

toil/test/wdl/standard_library/as_map.json

@@ -0,0 +1,16 @@
+{
+  "asMapWorkflow.in_array": [
+    {
+      "left": "a",
+      "right": 1
+    },
+    {
+      "left": "b",
+      "right": 2
+    },
+    {
+      "left": "c",
+      "right": 3
+    }
+  ]
+}

toil/test/wdl/standard_library/as_map_as_input.wdl

@@ -0,0 +1,23 @@
+version development
+
+workflow asMapWorkflow {
+  input {
+    Array[Pair[String, Int]] in_array
+  }
+
+  call copy_output {input: in_map=as_map(in_array)}
+}
+
+task copy_output {
+  input {
+    Map[String, Int] in_map
+  }
+
+  command {
+    cp ~{write_json(in_map)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/as_pairs.json

@@ -0,0 +1,7 @@
+{
+  "asPairsWorkflow.in_map": {
+    "a": 1,
+    "b": 2,
+    "c": 3
+  }
+}

toil/test/wdl/standard_library/as_pairs_as_input.wdl

@@ -0,0 +1,23 @@
+version development
+
+workflow asPairsWorkflow {
+  input {
+    Map[String, Int] in_map
+  }
+
+  call copy_output {input: in_pairs=as_pairs(in_map)}
+}
+
+task copy_output {
+  input {
+    Array[Pair[String, Int]] in_pairs
+  }
+
+  command {
+    cp ~{write_json(in_pairs)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/ceil.json

@@ -0,0 +1,3 @@
+{
+  "ceilWorkflow.num": 11.2345
+}

toil/test/wdl/standard_library/ceil_as_command.wdl

@@ -0,0 +1,16 @@
+workflow ceilWorkflow {
+  Float num
+  call get_ceil { input: num=num }
+}
+
+task get_ceil {
+  Float num
+
+  command {
+    echo ${ceil(num)} > output.txt
+  }
+
+ output {
+    File the_ceiling = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/ceil_as_input.wdl

@@ -0,0 +1,16 @@
+workflow ceilWorkflow {
+  Float num
+  call get_ceil { input: num=ceil(num) }
+}
+
+task get_ceil {
+  Float num
+
+  command {
+    echo ${num} > output.txt
+  }
+
+ output {
+    File the_ceiling = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/collect_by_key.json

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

toil/test/wdl/standard_library/collect_by_key_as_input.wdl

@@ -0,0 +1,23 @@
+version development
+
+workflow collectByKeyWorkflow {
+  input {
+    Array[Pair[String, Int]] in_array = [("a", 1), ("b", 2), ("a", 3)]
+  }
+
+  call copy_output {input: in_map=collect_by_key(in_array)}
+}
+
+task copy_output {
+  input {
+    Map[String, Array[Int]] in_map
+  }
+
+  command <<<
+    cp ~{write_json(in_map)} output.txt
+  >>>
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/cross.json

@@ -0,0 +1,11 @@
+{
+  "crossWorkflow.in_array_1": [
+    1,
+    2,
+    3
+  ],
+  "crossWorkflow.in_array_2": [
+    "a",
+    "b"
+  ]
+}

toil/test/wdl/standard_library/cross_as_input.wdl

@@ -0,0 +1,19 @@
+workflow crossWorkflow {
+  # this workflow depends on write_json()
+  Array[Int] in_array_1
+  Array[String] in_array_2
+
+  call copy_output {input: in_array=cross(in_array_1, in_array_2)}
+}
+
+task copy_output {
+  Array[Pair[Int, String]] in_array
+
+  command {
+    cp ${write_json(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/flatten.json

@@ -0,0 +1,7 @@
+{
+  "flattenWorkflow.in_array": [
+    [1, 2, 3],
+    [1],
+    [21, 22]
+  ]
+}

toil/test/wdl/standard_library/flatten_as_input.wdl

@@ -0,0 +1,18 @@
+workflow flattenWorkflow {
+  Array[Array[Int]] in_array
+
+  call copy_output {input: in_array=flatten(in_array)}
+}
+
+task copy_output {
+
+  Array[Int] in_array
+
+  command {
+    cp ${write_json(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/floor.json

@@ -0,0 +1,3 @@
+{
+  "floorWorkflow.num": 11.2345
+}

toil/test/wdl/standard_library/floor_as_command.wdl

@@ -0,0 +1,16 @@
+workflow floorWorkflow {
+  Float num
+  call get_floor { input: num=num }
+}
+
+task get_floor {
+  Float num
+
+  command {
+    echo ${floor(num)} > output.txt
+  }
+
+ output {
+    File the_flooring = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/floor_as_input.wdl

@@ -0,0 +1,16 @@
+workflow floorWorkflow {
+  Float num
+  call get_floor { input: num=floor(num) }
+}
+
+task get_floor {
+  Float num
+
+  command {
+    echo ${num} > output.txt
+  }
+
+ output {
+    File the_flooring = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/keys.json

@@ -0,0 +1,8 @@
+{
+  "keysWorkflow.in_map": {
+    "a": 1,
+    "b": 2,
+    "c": 3
+  }
+}
+

toil/test/wdl/standard_library/keys_as_input.wdl

@@ -0,0 +1,24 @@
+version development
+
+workflow keysWorkflow {
+  input {
+    Map[String, Int] in_map
+  }
+
+  call copy_output {input: in_array=keys(in_map)}
+}
+
+task copy_output {
+  input {
+    Array[String] in_array
+  }
+
+  command {
+    cp ~{write_json(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}
+

toil/test/wdl/standard_library/length.json

@@ -0,0 +1,7 @@
+{
+  "lengthWorkflow.in_array": [
+    1,
+    2,
+    3
+  ]
+}

toil/test/wdl/standard_library/length_as_input.wdl

@@ -0,0 +1,16 @@
+workflow lengthWorkflow {
+  Array[Int] in_array
+  call copy_output {input: num=length(in_array)}
+}
+
+task copy_output {
+  Int num
+
+  command {
+    echo ${num} > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/length_as_input_with_map.json

@@ -0,0 +1,7 @@
+{
+  "lengthWorkflow.in_map": {
+    "1": "a",
+    "2": "b",
+    "3": "c"
+  }
+}

toil/test/wdl/standard_library/length_as_input_with_map.wdl

@@ -0,0 +1,17 @@
+workflow lengthWorkflow {
+  # this workflow should throw an error. length() does not work with Map[X, Y].
+  Map[String, String] in_map
+  call copy_output {input: num=length(in_map)}
+}
+
+task copy_output {
+  Int num
+
+  command {
+    echo ${num} > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/length_invalid.json

@@ -0,0 +1,3 @@
+{
+  "lengthWorkflow.in_array": null
+}

toil/test/wdl/standard_library/range.json

@@ -0,0 +1,3 @@
+{
+  "rangeWorkflow.num": 8
+}

toil/test/wdl/standard_library/range_0.json

@@ -0,0 +1,3 @@
+{
+  "rangeWorkflow.num": 0
+}

toil/test/wdl/standard_library/range_as_input.wdl

@@ -0,0 +1,17 @@
+workflow rangeWorkflow {
+  # this workflow depends on write_lines()
+  Int num
+  call copy_output {input: in_array=range(num)}
+}
+
+task copy_output {
+  Array[Int] in_array
+
+  command {
+    cp ${write_lines(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/range_invalid.json

@@ -0,0 +1,3 @@
+{
+  "rangeWorkflow.num": -1
+}

toil/test/wdl/standard_library/read_boolean.json

@@ -0,0 +1,3 @@
+{
+  "readBooleanWorkflow.in_file": "src/toil/test/wdl/testfiles/test_boolean.txt"
+}

toil/test/wdl/standard_library/read_boolean_as_command.wdl

@@ -0,0 +1,17 @@
+workflow readBooleanWorkflow {
+  File in_file
+
+  call read_boolean {input: in_file=in_file}
+}
+
+task read_boolean {
+  File in_file
+
+  command {
+    echo "${read_boolean(in_file)}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/read_float.json

@@ -0,0 +1,3 @@
+{
+  "readFloatWorkflow.in_file": "src/toil/test/wdl/testfiles/test_float.txt"
+}

toil/test/wdl/standard_library/read_float_as_command.wdl

@@ -0,0 +1,17 @@
+workflow readFloatWorkflow {
+  File in_file
+
+  call read_float {input: in_file=in_file}
+}
+
+task read_float {
+  File in_file
+
+  command {
+    echo "${read_float(in_file)}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/read_int.json

@@ -0,0 +1,3 @@
+{
+  "readIntWorkflow.in_file": "src/toil/test/wdl/testfiles/test_int.txt"
+}

toil/test/wdl/standard_library/read_int_as_command.wdl

@@ -0,0 +1,17 @@
+workflow readIntWorkflow {
+  File in_file
+
+  call read_int {input: in_file=in_file}
+}
+
+task read_int {
+  File in_file
+
+  command {
+    echo "${read_int(in_file)}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/read_json.json

@@ -0,0 +1,3 @@
+{
+  "readJsonWorkflow.in_file": "src/toil/test/wdl/testfiles/test.json"
+}

toil/test/wdl/standard_library/read_json_as_output.wdl

@@ -0,0 +1,31 @@
+workflow readJsonWorkflow {
+  # this workflow depends on stdout() and write_lines()
+  File in_file
+
+  call read_json {input: in_file=in_file}
+  call copy_output {input: in_json=read_json.out_json}
+}
+
+task read_json {
+  File in_file
+
+  command {
+    cat ${in_file}
+  }
+
+  output {
+    Map[String, String] out_json = read_json(stdout())
+  }
+}
+
+task copy_output {
+  Map[String, String] in_json
+
+  command {
+    cp ${write_json(in_json)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/read_lines.json

@@ -0,0 +1,3 @@
+{
+  "readLinesWorkflow.in_file": "src/toil/test/wdl/testfiles/test_lines.txt"
+}

toil/test/wdl/standard_library/read_lines_as_output.wdl

@@ -0,0 +1,31 @@
+workflow readLinesWorkflow {
+  # this workflow depends on stdout() and write_lines()
+  File in_file
+
+  call read_lines {input: in_file=in_file}
+  call copy_output {input: in_array=read_lines.out_array}
+}
+
+task read_lines {
+  File in_file
+
+  command {
+    cat ${in_file}
+  }
+
+  output {
+    Array[String] out_array = read_lines(stdout())
+  }
+}
+
+task copy_output {
+  Array[String] in_array
+
+  command {
+    cp ${write_lines(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/read_map.json

@@ -0,0 +1,3 @@
+{
+  "readMapWorkflow.in_file": "src/toil/test/wdl/testfiles/test_map.txt"
+}