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Bug #13931

closed

[CWL] size field not accessible on arvados

Added by Jiayong Li over 6 years ago. Updated over 6 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
-
Target version:
Start date:
08/06/2018
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
-
Release:
Release relationship:
Auto

Description

Getting the cwl error.

2018-07-30T14:55:20.765294319Z cwltool ERROR: Execution failed: ../../lib/cwl/workflow.json:1:26: Expression evaluation error:
2018-07-30T14:55:20.765294319Z ../../lib/cwl/workflow.json:1:26: Syntax error in parameter reference 'inputs.fastq1.size': inputs.fastq1.size does not contain key 'size'. This could be due to using Javascript code without specifying InlineJavascriptRequirement.

cwl script as follows

cwlVersion: v1.0
class: CommandLineTool
inputs:
  fastq1: File
outputs:
  out: stdout
baseCommand: echo
arguments:
  - $(inputs.fastq1.size)
stdout: size.txt

Version

/data-sdd/home/jiayong/envs/acr/bin/arvados-cwl-runner 1.1.4.20180720151136,
arvados-python-client 1.1.4.20180720151136, cwltool 1.0.20180615183820


Subtasks 2 (0 open2 closed)

Task #13949: Review 13931-cwl-sizeResolvedTom Clegg08/06/2018

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Task #14023: Review 13931-uri-unquoteResolvedPeter Amstutz08/06/2018

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Related issues 1 (0 open1 closed)

Related to Arvados - Bug #14074: a-c-r does not work with input keep locators containing '#' charactersResolved

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