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conformance_tests.yaml
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# every "id" must be unique and have no spaces
# every "doc" must be unique
# "id" and "doc" should be meaningful
- job: tests/bwa-mem-job.json
tool: tests/bwa-mem-tool.cwl
output:
args: [bwa, mem, -t, '2', -I, '1,2,3,4', -m, '3',
chr20.fa,
example_human_Illumina.pe_1.fastq,
example_human_Illumina.pe_2.fastq]
id: cl_basic_generation
doc: General test of command line generation
tags: [ required, command_line_tool ]
- output:
args: [bwa, mem, chr20.fa,
"-XXX",
"-YYY", example_human_Illumina.pe_1.fastq,
"-YYY", example_human_Illumina.pe_2.fastq]
job: tests/bwa-mem-job.json
tool: tests/binding-test.cwl
id: nested_prefixes_arrays
doc: Test nested prefixes with arrays
tags: [ required, command_line_tool ]
- output:
args: [tmap, mapall, stage1, map1, --min-seq-length, '20', map2, --min-seq-length,
'20', stage2, map1, --max-seq-length, '20', --min-seq-length, '10', --seed-length,
'16', map2, --max-seed-hits, '-1', --max-seq-length, '20', --min-seq-length, '10']
job: tests/tmap-job.json
tool: tests/tmap-tool.cwl
id: nested_cl_bindings
doc: Test nested command line bindings
tags: [ schema_def, command_line_tool ]
- output:
args: [cat, hello.txt]
job: tests/cat-job.json
tool: tests/cat1-testcli.cwl
id: cl_optional_inputs_missing
doc: Test command line with optional input (missing)
tags: [ required, command_line_tool ]
- output:
args: [cat, -n, hello.txt]
job: tests/cat-n-job.json
tool: tests/cat1-testcli.cwl
id: cl_optional_bindings_provided
doc: Test command line with optional input (provided)
tags: [ required, command_line_tool ]
- output:
"foo": {
"checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
"class": "File",
"location": "foo.txt",
"size": 22
}
job: tests/cat-job.json
tool: tests/template-tool.cwl
id: initworkdir_expreng_requirements
doc: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature
tags: [ initial_work_dir, inline_javascript, command_line_tool ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat3-tool.cwl
id: stdout_redirect_docker
doc: Test command execution in Docker with stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/cat-job.json
tool: tests/cat3-tool-shortcut.cwl
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: Any
size: 13
id: stdout_redirect_shortcut_docker
doc: Test command execution in Docker with shortcut stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: cat-out
size: 13
tool: tests/cat3-tool-mediumcut.cwl
id: stdout_redirect_mediumcut_docker
doc: Test command execution in Docker with mediumcut stdout redirection
tags: [ docker, command_line_tool ]
- job: tests/empty.json
tool: tests/stderr.cwl
id: stderr_redirect
doc: Test command line with stderr redirection
output:
output_file:
class: File
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
size: 4
location: error.txt
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
tool: tests/stderr-shortcut.cwl
id: stderr_redirect_shortcut
doc: Test command line with stderr redirection, brief syntax
output:
output_file:
class: File
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
size: 4
location: Any
tags: [ shell_command, command_line_tool ]
- output:
output_file:
class: File
size: 4
checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
location: std.err
job: tests/empty.json
tool: tests/stderr-mediumcut.cwl
id: stderr_redirect_mediumcut
doc: Test command line with stderr redirection, named brief syntax
tags: [ shell_command, command_line_tool ]
- job: tests/cat-job.json
output:
output_txt:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat4-tool.cwl
id: stdinout_redirect_docker
doc: Test command execution in Docker with stdin and stdout redirection
tags: [ required, command_line_tool ]
- job: tests/empty.json
tool: tests/null-expression1-tool.cwl
output:
output: 1
id: expression_any
doc: Test default usage of Any in expressions.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression1-job.json
tool: tests/null-expression1-tool.cwl
output:
output: 1
id: expression_any_null
doc: Test explicitly passing null to Any type inputs with default values.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression2-job.json
tool: tests/null-expression1-tool.cwl
output:
output: 2
id: expression_any_string
doc: Testing the string 'null' does not trip up an Any with a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/empty.json
tool: tests/null-expression2-tool.cwl
should_fail: true
id: expression_any_nodefaultany
doc: Test Any without defaults cannot be unspecified.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression1-job.json
tool: tests/null-expression2-tool.cwl
should_fail: true
id: expression_any_null_nodefaultany
doc: Test explicitly passing null to Any type without a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/null-expression2-job.json
tool: tests/null-expression2-tool.cwl
output:
output: 2
id: expression_any_nullstring_nodefaultany
doc: Testing the string 'null' does not trip up an Any without a default value.
tags: [ inline_javascript, expression_tool ]
- job: tests/any-type-job.json
tool: tests/any-type-compat.cwl
output:
output1: ["hello", "world"]
output2: ["foo", "bar"]
output3: hello
id: any_outputSource_compatibility
doc: Testing Any type compatibility in outputSource
tags: [ required, workflow ]
- job: tests/cat-job.json
output:
output:
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
class: File
location: output
size: 13
tool: tests/cat-tool.cwl
id: stdinout_redirect
doc: Test command execution in with stdin and stdout redirection
tags: [ required, command_line_tool ]
- job: tests/parseInt-job.json
output: {output: 42}
tool: tests/parseInt-tool.cwl
id: expression_parseint
doc: Test ExpressionTool with Javascript engine
tags: [ inline_javascript, expression_tool ]
- job: tests/wc-job.json
output: {output: 16}
tool: tests/wc2-tool.cwl
id: expression_outputEval
doc: Test outputEval to transform output
tags: [ inline_javascript, command_line_tool ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines1-wf.cwl
id: wf_wc_parseInt
doc: Test two step workflow with imported tools
tags: [ inline_javascript, workflow ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines2-wf.cwl
id: wf_wc_expressiontool
doc: Test two step workflow with inline tools
tags: [ inline_javascript, workflow ]
- job: tests/count-lines3-job.json
output:
count_output: [16, 1]
tool: tests/count-lines3-wf.cwl
id: wf_wc_scatter
doc: Test single step workflow with Scatter step
tags: [ scatter, inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: [16, 1]
tool: tests/count-lines4-wf.cwl
id: wf_wc_scatter_multiple_merge
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, default merge behavior
tags: [ scatter, multiple_input, inline_javascript, workflow ]
- job: tests/count-lines6-job.json
output:
count_output: [32, 2]
tool: tests/count-lines6-wf.cwl
id: wf_wc_scatter_multiple_nested
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, nested merge behavior
tags: [ scatter, multiple_input, inline_javascript, workflow ]
- job: tests/count-lines6-job.json
output:
count_output: 34
tool: tests/count-lines7-wf.cwl
id: wf_wc_scatter_multiple_flattened
doc: >-
Test single step workflow with Scatter step and two data links connected to
same input, flattened merge behavior
tags: [ multiple_input, inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: 16
tool: tests/count-lines13-wf.cwl
id: wf_wc_nomultiple
doc: >-
Test when step source is a single-item list and there is no
linkMerge, then it not wrapped in a list, and that
MultipleInputFeatureRequirement is not required.
tags: [ inline_javascript, workflow ]
- job: tests/count-lines4-job.json
output:
count_output: 16
tool: tests/count-lines19-wf.cwl
id: wf_wc_nomultiple_merge_nested
doc: >-
Test when step source is a single-item list and linkMerge is
listed, then it is wrapped in a list.
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {count_output: 1}
tool: tests/count-lines5-wf.cwl
id: wf_input_default_missing
doc: Test workflow with default value for input parameter (missing)
tags: [ inline_javascript, workflow ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines5-wf.cwl
id: wf_input_default_provided
doc: Test workflow with default value for input parameter (provided)
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {default_output: workflow_default}
tool: tests/echo-wf-default.cwl
id: wf_default_tool_default
doc: Test that workflow defaults override tool defaults
tags: [ required, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
location: out
size: 15
tool: tests/env-tool1.cwl
id: envvar_req
doc: Test EnvVarRequirement
tags: [ env_var, command_line_tool ]
- job: tests/scatter-job1.json
output:
out: ["foo one", "foo two", "foo three", "foo four"]
tool: tests/scatter-wf1.cwl
id: wf_scatter_single_param
doc: Test workflow scatter with single scatter parameter
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: [["foo one three", "foo one four"], ["foo two three", "foo two four"]]
tool: tests/scatter-wf2.cwl
id: wf_scatter_two_nested_crossproduct
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: ["foo one three", "foo one four", "foo two three", "foo two four"]
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_two_flat_crossproduct
doc: Test workflow scatter with two scatter parameters and flat_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-job2.json
output:
out: ["foo one three", "foo two four"]
tool: "tests/scatter-wf4.cwl#main"
id: wf_scatter_two_dotproduct
doc: Test workflow scatter with two scatter parameters and dotproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job1.json
output:
out: []
tool: tests/scatter-wf1.cwl
id: wf_scatter_emptylist
doc: Test workflow scatter with single empty list parameter
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job2.json
output:
out: [[], []]
tool: tests/scatter-wf2.cwl
id: wf_scatter_nested_crossproduct_secondempty
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job3.json
output:
out: []
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_nested_crossproduct_firstempty
doc: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job2.json
output:
out: []
tool: "tests/scatter-wf3.cwl#main"
id: wf_scatter_flat_crossproduct_oneempty
doc: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method
tags: [ scatter, workflow ]
- job: tests/scatter-empty-job4.json
output:
out: []
tool: "tests/scatter-wf4.cwl#main"
id: wf_scatter_dotproduct_twoempty
doc: Test workflow scatter with two empty scatter parameters and dotproduct join method
tags: [ scatter, workflow ]
- tool: tests/echo-tool.cwl
job: tests/env-job.json
output:
{"out": "hello test env\n"}
id: any_input_param
doc: Test Any type input parameter
tags: [ required, command_line_tool ]
- job: tests/wc-job.json
output: {count_output: 16}
tool: tests/count-lines8-wf.cwl
id: nested_workflow
doc: Test nested workflow
tags: [ subworkflow, workflow, inline_javascript ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
location: out
size: 15
tool: tests/env-wf1.cwl
id: requirement_priority
doc: Test requirement priority
tags: [ env_var, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
location: out
size: 9
tool: tests/env-wf2.cwl
id: requirement_override_hints
doc: Test requirements override hints
tags: [ env_var, workflow ]
- job: tests/env-job.json
output:
out:
class: File
checksum: sha1$cdc1e84968261d6a7575b5305945471f8be199b6
location: out
size: 9
tool: tests/env-wf3.cwl
id: requirement_workflow_steps
doc: Test requirements on workflow steps
tags: [ env_var, workflow ]
- job: tests/empty.json
output: {count_output: 16}
tool: tests/count-lines9-wf.cwl
id: step_input_default_value
doc: Test default value on step input parameter
tags: [ inline_javascript, workflow ]
- job: tests/empty.json
output: {count_output: 16}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_nosource
doc: Test use default value on step input parameter with empty source
tags: [ inline_javascript, workflow ]
- job: tests/file1-null.json
output: {count_output: 16}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_nullsource
doc: Test use default value on step input parameter with null source
tags: [ inline_javascript, workflow ]
- job: tests/cat-job.json
output: {count_output: 1}
tool: tests/count-lines11-wf.cwl
id: step_input_default_value_overriden
doc: Test default value on step input parameter overridden by provided source
tags: [ inline_javascript, workflow ]
- job: tests/revsort-job.json
output:
output:
class: File
checksum: sha1$b9214658cc453331b62c2282b772a5c063dbd284
location: output.txt
size: 1111
tool: tests/revsort.cwl
id: wf_simple
doc: Test simple workflow
tags: [ required, workflow ]
- job: tests/cat-job.json
output:
output_file:
class: File
checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
location: output.txt
size: 13
tool: tests/cat5-tool.cwl
id: hints_unknown_ignored
doc: Test unknown hints are ignored.
tags: [ required, command_line_tool ]
- job: tests/search-job.json
output:
outfile:
class: File
checksum: sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0
location: result.txt
size: 142
indexedfile: {
"location": "input.txt",
"class": "File",
"checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
"secondaryFiles": [
{
"location": "input.txt.idx1",
"class": "File",
"checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
"size": 1500
},
{
"location": "input.idx2",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx3",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx4",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.txt.idx5",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"location": "input.idx6.txt",
"class": "File",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"size": 0
},
{
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "input.txt.idx7",
"size": 0
},
{
"checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
"class": "File",
"location": "hello.txt",
"size": 13
},
{
"class": "Directory",
"listing": [{
"basename": "index",
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"class": "File",
"location": "index",
"size": 0
}],
"location": "input.txt_idx8",
}
],
"size": 1111
}
tool: "tests/search.cwl#main"
id: initial_workdir_secondary_files_expr
doc: >-
Test InitialWorkDirRequirement linking input files and capturing secondaryFiles
on input and output. Also tests the use of a variety of parameter references
and expressions in the secondaryFiles field.
tags: [ initial_work_dir, inline_javascript, workflow ]
- job: tests/rename-job.json
output:
outfile:
class: File
checksum: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
location: fish.txt
size: 1111
tool: tests/rename.cwl
id: rename
doc: >-
Test InitialWorkDirRequirement with expression in filename.
tags: [ initial_work_dir, command_line_tool ]
- job: tests/string-job.json
output:
out:
class: File
checksum: sha1$6a47aa22b2a9d13a66a24b3ee5eaed95ce4753cf
location: example.conf
size: 16
tool: tests/iwdr-entry.cwl
id: initial_workdir_trailingnl
doc: Test if trailing newline is present in file entry in InitialWorkDir
tags: [ initial_work_dir, command_line_tool ]
- job: tests/wc-job.json
output:
output: 16
tool: tests/wc4-tool.cwl
id: inline_expressions
doc: >-
Test inline expressions
tags: [ inline_javascript, command_line_tool ]
- job: tests/schemadef-job.json
output:
output:
location: output.txt
size: 12
class: File
checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
tool: tests/schemadef-tool.cwl
id: schemadef_req_tool_param
doc: >-
Test SchemaDefRequirement definition used in tool parameter
tags: [ schema_def, command_line_tool ]
- job: tests/schemadef-job.json
output:
output:
location: output.txt
size: 12
class: File
checksum: "sha1$f12e6cfe70f3253f70b0dbde17c692e7fb0f1e5e"
tool: tests/schemadef-wf.cwl
id: schemadef_req_wf_param
doc: >-
Test SchemaDefRequirement definition used in workflow parameter
tags: [ schema_def, workflow ]
- job: tests/empty.json
output: {
"t1": {
"bar": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
}
},
"t10": true,
"t11": true,
"t12": null,
"t13": "-zab1",
"t14": "-zab1",
"t15": "-zab1",
"t16": "-zab1",
"t17": "zab1 zab1",
"t18": "zab1 zab1",
"t19": "zab1 zab1",
"t2": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t20": "zab1 zab1",
"t21": "2 2",
"t22": "true true",
"t23": "true true",
"t24": "null null",
"t25": "b",
"t26": "b b",
"t3": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t4": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t5": "zab1",
"t6": "zab1",
"t7": "zab1",
"t8": "zab1",
"t9": 2,
"t27": null,
"t28": 3
}
tool: tests/params.cwl
id: param_evaluation_noexpr
doc: Test parameter evaluation, no support for JS expressions
tags: [ required, command_line_tool ]
- job: tests/empty.json
output: {
"t1": {
"bar": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
}
},
"t10": true,
"t11": true,
"t12": null,
"t13": "-zab1",
"t14": "-zab1",
"t15": "-zab1",
"t16": "-zab1",
"t17": "zab1 zab1",
"t18": "zab1 zab1",
"t19": "zab1 zab1",
"t2": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t20": "zab1 zab1",
"t21": "2 2",
"t22": "true true",
"t23": "true true",
"t24": "null null",
"t25": "b",
"t26": "b b",
"t3": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t4": {
"b az": 2,
"b\"az": null,
"b'az": true,
"baz": "zab1",
"buz": [
"a",
"b",
"c"
]
},
"t5": "zab1",
"t6": "zab1",
"t7": "zab1",
"t8": "zab1",
"t9": 2,
"t27": null,
"t28": 3
}
tool: tests/params2.cwl
id: param_evaluation_expr
doc: >-
Test parameter evaluation, with support for JS expressions
tags: [ inline_javascript, command_line_tool ]
- output: {}
job: tests/cat-job.json
tool: tests/metadata.cwl
id: metadata
doc: Test metadata
tags: [ required, command_line_tool ]
- job: tests/formattest-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_2330"
"size": 1111
"class": "File"
"checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f"
tool: tests/formattest.cwl
id: format_checking
doc: >-
Test simple format checking.
tags: [ required, command_line_tool ]
- job: tests/formattest2-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_1929"
"size": 12010
"class": "File"
"checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
tool: tests/formattest2.cwl
id: format_checking_subclass
doc: >-
Test format checking against ontology using subclassOf.
tags: [ required, command_line_tool ]
- job: tests/formattest2-job.json
output:
output:
"location": "output.txt"
"format": "http://edamontology.org/format_1929"
"size": 12010
"class": "File"
"checksum": "sha1$971d88faeda85a796752ecf752b7e2e34f1337ce"
tool: tests/formattest3.cwl
id: format_checking_equivalentclass
doc: >-
Test format checking against ontology using equivalentClass.
tags: [ required, command_line_tool ]
- tool: tests/optional-output.cwl
job: tests/cat-job.json
output:
optional_file: null
output_file:
location: output.txt
size: 13
class: "File"
checksum: "sha1$47a013e660d408619d894b20806b1d5086aab03b"
id: output_secondaryfile_optional
doc: >-
Test optional output file and optional secondaryFile on output.
tags: [ docker, command_line_tool ]
- job: tests/empty.json
output:
out: "\n"
tool: tests/vf-concat.cwl
id: valuefrom_ignored_null
doc: Test that valueFrom is ignored when the parameter is null
tags: [ inline_javascript, command_line_tool ]
- job: tests/cat-job.json
output:
out: "a string\n"
tool: tests/vf-concat.cwl
id: valuefrom_secondexpr_ignored
doc: Test that second expression in concatenated valueFrom is not ignored
tags: [ inline_javascript, command_line_tool ]
- job: tests/step-valuefrom-wf.json
output: {count_output: 16}
tool: tests/step-valuefrom-wf.cwl
id: valuefrom_wf_step
doc: Test valueFrom on workflow step.
tags: [ step_input, inline_javascript, workflow ]
- job: tests/step-valuefrom-job.json
output: {val: "3\n"}
tool: tests/step-valuefrom2-wf.cwl
id: valuefrom_wf_step_multiple
doc: Test valueFrom on workflow step with multiple sources
tags: [ step_input, inline_javascript, multiple_input, workflow ]
- job: tests/step-valuefrom-job.json
output: {val: "3\n"}
tool: tests/step-valuefrom3-wf.cwl
id: valuefrom_wf_step_other
doc: Test valueFrom on workflow step referencing other inputs
tags: [ step_input, inline_javascript, workflow ]
- job: tests/record-output-job.json
output:
"orec": {
"ofoo": {
"location": "foo",
"size": 1111,
"class": "File",
"checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"
},
"obar": {
"location": "bar",
"size": 12010,
"class": "File",
"checksum": "sha1$aeb3d11bdf536511649129f4077d5cda6a324118"
}
}
tool: tests/record-output.cwl
id: record_output_binding
doc: Test record type output binding.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out.cwl
id: docker_json_output_path
doc: >-
Test support for reading cwl.output.json when running in a Docker container
and just 'path' is provided.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out2.cwl
id: docker_json_output_location
doc: >-
Test support for reading cwl.output.json when running in a Docker container
and just 'location' is provided.
tags: [ shell_command, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out3.cwl
id: json_output_path_relative
doc: >-
Test support for reading cwl.output.json where 'path' is relative path in output dir.
tags: [ required, command_line_tool ]
- job: tests/empty.json
output: {
"foo": {
"location": "foo",
"class": "File",
"checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15",
"size": 4
}
}
tool: tests/test-cwl-out4.cwl
id: json_output_location_relative
doc: >-
Test support for reading cwl.output.json where 'location' is relative reference to output dir.
tags: [ required, command_line_tool ]
- job: tests/abc.json
output:
files: [{
"location": "a",
"size": 0,
"class": "File",