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WorkflowStepInput.valueFrom: if self is type Directory, then `self.… #750

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WorkflowStepInput.valueFrom: if self is type Directory, then `self.… #750

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WorkflowStepInput.valueFrom: if self is type `Directory`, then `self.…
mr-c Jul 27, 2018
14d0834
Merge branch 'master' into workflowstepinput.valuefrom_directory.listing
stain Nov 16, 2018
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15 changes: 15 additions & 0 deletions v1.0/conformance_test_v1.0.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -1862,3 +1862,18 @@
inputs are not present in the input object used to run the tool.
should_fail: true
tags: [ required, workflow ]

- job: v1.0/dir3-job.yml
tool: v1.0/single_file_from_dir.cwl
label: step_input_directory_listing
id: 133
doc: >
WorkflowStepInput.valueFrom: if self is type `Directory`, then
`self.listing` should be present
output:
output:
class: File
basename: output
size: 24
checksum: sha1$dd0a4c4c49ba43004d6611771972b6cf969c1c01
tags: [ step_input, workflow ]
28 changes: 28 additions & 0 deletions v1.0/v1.0/single_file_from_dir.cwl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow

requirements:
StepInputExpressionRequirement: {}

inputs:
inf: File # tarfile
outputs:
output:
type: File
outputSource: second/output

steps:
first:
run: dir3.cwl
in:
inf: inf
out: [ outdir ]
second:
run: cat-tool.cwl
in:
file1:
source: first/outdir
valueFrom: $(self.listing[0])
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Can you access the file by a name? The index might not be very reliable or desired.

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not as easily as one would have to filter on basename - but this test only needs to verify that self.listing is populated and so [0] should be present.

out: [ output ]