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

toil/test/wdl/standard_library/read_map_as_output.wdl

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

toil/test/wdl/standard_library/read_string.json

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

toil/test/wdl/standard_library/read_string_as_command.wdl

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

toil/test/wdl/standard_library/read_tsv.json

@@ -0,0 +1,3 @@
+{
+  "readTsvWorkflow.in_file": "src/toil/test/wdl/test.tsv"
+}

toil/test/wdl/standard_library/read_tsv_as_output.wdl

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

toil/test/wdl/standard_library/round.json

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

toil/test/wdl/standard_library/round_as_command.wdl

@@ -0,0 +1,16 @@
+workflow roundWorkflow {
+  Float num
+  call get_round { input: num=num }
+}
+
+task get_round {
+  Float num
+
+  command {
+    echo ${round(num)} > output.txt
+  }
+
+ output {
+    File the_rounding = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/round_as_input.wdl

@@ -0,0 +1,16 @@
+workflow roundWorkflow {
+  Float num
+  call get_round { input: num=round(num) }
+}
+
+task get_round {
+  Float num
+
+  command {
+    echo ${num} > output.txt
+  }
+
+ output {
+    File the_rounding = 'output.txt'
+ }
+}

toil/test/wdl/standard_library/size.json

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

toil/test/wdl/standard_library/size_as_command.wdl

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

toil/test/wdl/standard_library/size_as_output.wdl

@@ -0,0 +1,36 @@
+workflow sizeWorkflow {
+  call get_size
+  call copy_output {
+    input:
+      float_0 = get_size.created_file_size,
+      float_1 = get_size.created_file_size_in_KB,
+      float_2 = get_size.created_file_size_in_KiB
+  }
+}
+
+task get_size {
+
+  command {
+    echo "this file is 22 bytes" > created_file
+  }
+
+  output {
+    Float created_file_size = size("created_file") # 22.0
+    Float created_file_size_in_KB = size("created_file", "K") # 0.022
+    Float created_file_size_in_KiB = size("created_file", "Ki") # 0.021484375
+  }
+}
+
+task copy_output {
+  Float float_0
+  Float float_1
+  Float float_2
+
+  command {
+    echo "${float_0} ${float_1} ${float_2}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/stderr.json

@@ -0,0 +1,3 @@
+{
+  "stderrWorkflow.message": "a journey straight to stderr"
+}

toil/test/wdl/standard_library/stderr_as_output.wdl

@@ -0,0 +1,30 @@
+workflow stderrWorkflow {
+  String message
+  call get_stderr { input: message=message }
+  call copy_output { input: in_file=get_stderr.check_this }
+}
+
+task get_stderr {
+  String message
+
+  command {
+    >&2 echo "${message}"
+  }
+
+  output {
+    File check_this = stderr()
+  }
+}
+
+# comply with builtinTest
+task copy_output {
+  File in_file
+
+  command {
+    cp ${in_file} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/stdout.json

@@ -0,0 +1,3 @@
+{
+  "stdoutWorkflow.message": "A Whale of a Tale."
+}

toil/test/wdl/standard_library/stdout_as_output.wdl

@@ -0,0 +1,30 @@
+workflow stdoutWorkflow {
+  String message
+  call get_stdout { input: message=message }
+  call copy_output { input: in_file=get_stdout.check_this }
+}
+
+task get_stdout {
+  String message
+
+  command {
+    echo "${message}"
+  }
+
+  output {
+    File check_this = stdout()
+ }
+}
+
+# comply with builtinTest
+task copy_output {
+  File in_file
+
+  command {
+    cp ${in_file} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/sub.json

@@ -0,0 +1,3 @@
+{
+  "subWorkflow.in_file": "src/toil/test/wdl/test.tsv"
+}

toil/test/wdl/standard_library/sub_as_input.wdl

@@ -0,0 +1,17 @@
+workflow subWorkflow {
+  String in_file
+  call get_sub {input: in_file=in_file}
+}
+
+task get_sub {
+  String in_file
+  String out_file_name = sub(in_file, "\\.tsv$", ".csv")
+
+  command {
+    echo "${out_file_name}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/sub_as_input_with_file.wdl

@@ -0,0 +1,17 @@
+workflow subWorkflow {
+  File in_file
+  call get_sub {input: in_file=in_file}
+}
+
+task get_sub {
+  File in_file
+  String out_file_name = sub(in_file, "\\.tsv$", ".csv")
+
+  command {
+    echo "${out_file_name}" > output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/transpose.json

@@ -0,0 +1,6 @@
+{
+  "transposeWorkflow.in_array": [
+    [0, 1, 2],
+    [3, 4, 5]
+  ]
+}

toil/test/wdl/standard_library/transpose_as_input.wdl

@@ -0,0 +1,18 @@
+workflow transposeWorkflow {
+  # this workflow depends on write_tsv()
+  Array[Array[Int]] in_array
+
+  call copy_output {input: in_array=transpose(in_array)}
+}
+
+task copy_output {
+  Array[Array[Int]] in_array
+
+  command {
+    cp ${write_tsv(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/write_json.json

@@ -0,0 +1,6 @@
+{
+  "writeJsonWorkflow.in_map": {
+    "key1": "value1",
+    "key2": "value2"
+  }
+}

toil/test/wdl/standard_library/write_json_as_command.wdl

@@ -0,0 +1,17 @@
+workflow writeJsonWorkflow {
+  Map[String, String] in_map
+
+  call write_json {input: in_map=in_map}
+}
+
+task write_json {
+  Map[String, String] in_map
+
+  command {
+    cp ${write_json(in_map)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/write_lines.json

@@ -0,0 +1,7 @@
+{
+  "writeLinesWorkflow.in_array": [
+    "first",
+    "second",
+    "third"
+  ]
+}

toil/test/wdl/standard_library/write_lines_as_command.wdl

@@ -0,0 +1,17 @@
+workflow writeLinesWorkflow {
+  Array[String] in_array
+
+  call write_lines {input: in_array=in_array}
+}
+
+task write_lines {
+  Array[String] in_array
+
+  command {
+    cp ${write_lines(in_array)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/write_map.json

@@ -0,0 +1,6 @@
+{
+  "writeMapWorkflow.in_map": {
+    "key1": "value1",
+    "key2": "value2"
+  }
+}

toil/test/wdl/standard_library/write_map_as_command.wdl

@@ -0,0 +1,17 @@
+workflow writeMapWorkflow {
+  Map[String, String] in_map
+
+  call write_map {input: in_map=in_map}
+}
+
+task write_map {
+  Map[String, String] in_map
+
+  command {
+    cp ${write_map(in_map)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/write_tsv.json

@@ -0,0 +1,6 @@
+{
+  "writeTsvWorkflow.in_tsv": [
+    ["one", "two", "three"],
+    ["un", "deux", "trois"]
+  ]
+}

toil/test/wdl/standard_library/write_tsv_as_command.wdl

@@ -0,0 +1,17 @@
+workflow writeTsvWorkflow {
+  Array[Array[String]] in_tsv
+
+  call write_tsv {input: in_tsv=in_tsv}
+}
+
+task write_tsv {
+  Array[Array[String]] in_tsv
+
+  command {
+    cp ${write_tsv(in_tsv)} output.txt
+  }
+
+  output {
+    File the_output = 'output.txt'
+  }
+}

toil/test/wdl/standard_library/zip.json

@@ -0,0 +1,12 @@
+{
+  "zipWorkflow.in_array_1": [
+    1,
+    2,
+    3
+  ],
+  "zipWorkflow.in_array_2": [
+    "a",
+    "b",
+    "c"
+  ]
+}

toil/test/wdl/standard_library/zip_as_input.wdl

@@ -0,0 +1,19 @@
+workflow zipWorkflow {
+  # this workflow depends on write_json()
+  Array[Int] in_array_1
+  Array[String] in_array_2
+
+  call copy_output {input: in_array=zip(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/test.csv

@@ -0,0 +1,3 @@
+1,2,3
+4,5,6
+7,8,9

toil/test/wdl/test.tsv

@@ -0,0 +1,3 @@
+1	2	3
+4	5	6
+7	8	9

toil/test/wdl/testfiles/croo.wdl

@@ -0,0 +1,38 @@
+version 1.0
+
+workflow wf {
+    meta {
+        # Advertise as needing the Cromwell Output Organizer
+        croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/atac.croo.v5.json'
+    }
+
+    input {
+    }
+
+    call do_math {
+    input:
+        number = 3
+    }
+
+    Int should_never_output = do_math.cube - 1
+
+    output {
+        Int only_result = do_math.square
+    }
+}
+
+task do_math {
+    input {
+        Int number
+    }
+    
+    # Not allowed to not have a command
+    command <<<
+    >>>
+
+    output {
+        Int square = number * number
+        Int cube = number * number * number
+    }
+}
+

toil/test/wdl/testfiles/drop_files.wdl

@@ -0,0 +1,62 @@
+version 1.0
+
+import "drop_files_subworkflow.wdl" as subwf
+
+# Workflow for testing discarding un-output files at the end of a workflow.
+# Does a bunch of unusual things with files.
+workflow wf {
+    input {
+        File file_in
+        File? file_in_default = "localfile.txt"
+    }
+
+    call make_file {
+    input:
+        number = 3,
+        needed_only_for_task = write_lines(["This file is consumed by a task call"])
+    }
+    
+    File will_discard = write_lines(["This file should be discarded"])
+    File will_keep = write_lines(["This file should be kept"])
+    File will_keep_because = will_keep
+
+    call subwf.subwf {
+    input:
+        kept_file = write_lines(["This file is kept by a subworkflow"]),
+        # Even though we pass will_keep to the subworkflow and it doesn't output it, it should not get deleted.
+        dropped_files = [write_lines(["This file is dropped by a subworkflow"]), will_keep]
+    }
+
+    File will_remember_one_of = select_first([write_lines(["This file gets stored in a variable"]), write_lines(["This file never gets stored in a variable"])])
+
+    output {
+        Array[File] files_kept = [make_file.out_file_1, make_file.out_file_2, will_keep_because, subwf.keep]
+    }
+}
+
+task make_file {
+    input {
+        Int number = 5
+        File needed_only_for_task
+        File file_with_default = write_lines(["This file is created in a task inputs section"])
+    }
+    
+    command <<<
+        echo ~{number}
+        echo "This file is collected as a task output twice" >testfile.txt
+        echo "This task file is not used" >badfile.txt
+    >>>
+
+    runtime {
+        runtime_file: write_lines(["This file is created in a runtime section"])
+    }
+
+    output {
+        File out_file_1 = stdout()
+        File out_file_2 = "testfile.txt"
+        File out_file_3 = "testfile.txt"
+        File out_file_4 = write_lines(["Again", "~{number}"])
+        File out_file_5 = "badfile.txt"
+    }
+}
+

toil/test/wdl/testfiles/drop_files_subworkflow.wdl

@@ -0,0 +1,13 @@
+version 1.0
+
+workflow subwf {
+    input {
+        File kept_file
+        Array[File] dropped_files
+    }
+
+    output {
+        File keep = kept_file
+    }
+}
+

toil/test/wdl/testfiles/not_enough_outputs.wdl

@@ -0,0 +1,33 @@
+version 1.0
+
+workflow wf {
+    input {
+    }
+
+    call do_math {
+    input:
+        number = 3
+    }
+
+    Int should_never_output = do_math.cube - 1
+
+    output {
+        Int only_result = do_math.square
+    }
+}
+
+task do_math {
+    input {
+        Int number
+    }
+    
+    # Not allowed to not have a command
+    command <<<
+    >>>
+
+    output {
+        Int square = number * number
+        Int cube = number * number * number
+    }
+}
+