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WIP Remove baseCommand items with space from tests #847

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WIP Remove baseCommand items with space from tests #847

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d3c6948
Remove baseCommand items with space from tests
bogdang989 Apr 3, 2019
43da205
Fix EnvVarRequirement tests
bogdang989 Apr 3, 2019
bd7c7e5
Add appropriate tags to modified tests
bogdang989 Apr 3, 2019
ae10e8d
Simplify tests. Fix double hints in test.
bogdang989 Apr 3, 2019
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10 changes: 5 additions & 5 deletions v1.0/conformance_test_v1.0.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -352,7 +352,7 @@
label: envvar_req
id: 34
doc: Test EnvVarRequirement
tags: [ env_var, command_line_tool ]
tags: [ env_var, shell_command, command_line_tool ]

- job: v1.0/scatter-job1.json
output:
Expand Down Expand Up @@ -463,7 +463,7 @@
label: requirement_priority
id: 46
doc: Test requirement priority
tags: [ env_var, workflow ]
tags: [ env_var, shell_command, workflow ]

- job: v1.0/env-job.json
output:
Expand All @@ -476,7 +476,7 @@
label: requirement_override_hints
id: 47
doc: Test requirements override hints
tags: [ env_var, workflow ]
tags: [ env_var, shell_command, workflow ]

- job: v1.0/env-job.json
output:
Expand All @@ -489,7 +489,7 @@
label: requirement_workflow_steps
id: 48
doc: Test requirements on workflow steps
tags: [ env_var, workflow ]
tags: [ env_var, shell_command, workflow ]

- job: v1.0/empty.json
output: {count_output: 16}
Expand Down Expand Up @@ -1433,7 +1433,7 @@
label: hints_import
id: 104
doc: Test hints with $import
tags: [ required, command_line_tool ]
tags: [ required, env_var, shell_command, command_line_tool ]

- output: {}
job: v1.0/default_path_job.yml
Expand Down
7 changes: 6 additions & 1 deletion v1.0/v1.0/docker-run-cmd.cwl
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Expand Up @@ -12,4 +12,9 @@ outputs:
type: File
outputBinding:
glob: cow
baseCommand: ["-c", "echo 'moo' > cow"]

arguments:
- valueFrom: "-c"
position: 0
- valueFrom: "echo 'moo' > cow"
position: 1
7 changes: 5 additions & 2 deletions v1.0/v1.0/env-tool1.cwl
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Expand Up @@ -15,7 +15,10 @@ requirements:
EnvVarRequirement:
envDef:
TEST_ENV: $(inputs.in)
ShellCommandRequirement: {}

baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]
arguments:
- valueFrom: "echo $TEST_ENV > out"
position: 3
shellQuote: false

stdout: out
8 changes: 5 additions & 3 deletions v1.0/v1.0/env-tool2.cwl
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Expand Up @@ -14,7 +14,9 @@ hints:
EnvVarRequirement:
envDef:
TEST_ENV: $(inputs.in)
ShellCommandRequirement: {}

baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]

stdout: out
arguments:
- valueFrom: "echo $TEST_ENV > out"
position: 3
shellQuote: false
16 changes: 11 additions & 5 deletions v1.0/v1.0/imported-hint.cwl
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@@ -1,16 +1,22 @@
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
hints:

requirements:
ShellCommandRequirement: {}
ResourceRequirement:
ramMin: 8
inputs: []
outputs:
out: stdout
out:
type: File
outputBinding:
glob: out

hints:
- $import: envvar.yml

baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]

stdout: out
arguments:
- valueFrom: "echo $TEST_ENV > out"
position: 3
shellQuote: false