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broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Using relative pathnames in the input json file cause files to be copied when cromwell is executing on local backend #764

Closed LeeTL1220 closed 8 years ago

LeeTL1220 commented 8 years ago

json input to wdl script:

...
  "case_gatk_acnv_workflow.normal_bam_idx": "/crsp/scratch/recapseg/recapseg_validation_sample_bams_EEW_topoff/SM-74NEG.bam.bai",
  "case_gatk_acnv_workflow.jar_file": "gatk-protected.jar",
...

In this case gatk-protected.jar (local to the execution command) will be copied into the cromwell-execution dir, but the bam index will not.

LeeTL1220 commented 8 years ago

Desired behavior would be symlink for both files.

scottfrazer commented 8 years ago

Lee, which version of Cromwell?

LeeTL1220 commented 8 years ago

That custom jar file I got. Which I believe is between 0.19.2 and 0.19.3...

scottfrazer commented 8 years ago

This appears to be fixed on our 'develop' branch