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cromwell: support relative file paths in input JSON
See original GitHub issueCurrently, relative input paths are only supported when provided as command-line arguments, where they are translated to absolute paths. Providing relative input paths in the inputs JSON file passes them on unchanged and fails when trying to find them relative to the created cromwell folder:
Could not localize data/mockdata/seqs/First2000seqs_R1.fq -> /Users/.../20190830_101132_Workflow/cromwell/cromwell-executions/Workflow/ec53e465-8581-4027-bf54-f6c85e1deee9/call-Task/shard-1/inputs/46135967/First2000seqs_R1.fq:
data/mockdata/seqs/First2000seqs_R1.fq doesn't exist
Issue Analytics
- State:
- Created 4 years ago
- Comments:5
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@prihoda This should be fixed up in v0.4.1. Thanks!
@mlin I would make it relative to the cwd, so that it is equivalent to supplying the file as command line argument. Cromwell also considers paths to be relative to cwd.