Fix Travis #112
Fix Travis #112
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…#91) * Add metadata to workflows published on dockstore (#89) * add metadata to u_of_michigan_aligner.wdl * add metadata to FunctionalEquivalence.wdl * add metadata for topmed_freeze3_calling.wdl * add metadata sbg-alignment-cwl/topmed-alignment.cwl * add metadata functional equivalent aligner: /topmed-cwl/workflow/alignment_workflow.cwl * add metadata to topmed_freeze3_calling.cwl * add metadata topmed_variant_calling_pipeline.cwl * update raw imports for 1.32.0 release (#90)
align steps fails due to unbound variable; likely an issue in the handoff of the output of the prealign step See comments for the float/int workarounds needed
Confirmed to run locally
Feature wdl1.0
…thub-apps Feature/3694/migrate to GitHub apps
Runtime attribute disk_size requires type int in its string. Previously we kind of cheated by using strings to coerce a float into an int. With the built-in ceil() we can now make things a lot simplier. Ceil() will of course round up, but that was the end result of the string hack anyway.
untested, this push is needed to test on Terra
continuation of previous commit
Implements WDL 1.0 for the aligner and its two checker WDL files. Aligner and checker are confirmed to work on Terra with the included gs inputs.
| workflows: | ||
| - subclass: WDL | ||
| primaryDescriptorPath: /variant-caller/variant-caller-wdl/topmed_freeze3_calling.wdl | ||
| testParameterFiles: |
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don't you want to use the newer https://github.com/DataBiosphere/topmed-workflow-variant-calling?
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Good spot, thanks!
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Actually since that's a different repo I'm a little hesistant. Does that one have its own page on Dockstore?
| version 1.0 | ||
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| import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/master/aligner/u_of_michigan_aligner/u_of_michigan_aligner.wdl" as TopMed_aligner | ||
| import "https://raw.githubusercontent.com/DataBiosphere/topmed-workflows/master/aligner/u_of_michigan_aligner-checker/u_of_michigan_aligner_checker_calculation.wdl" as checker |
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Does using 'master' mean TravisCI will only be pulling in the latest released WDLs? I guess maybe there isn't a better way to do this until relative imports are supported in Terra so they can be used here?
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I don't remember all the details, but if I recall correctly, it has to be master because 1.32.0 is out of date and doesn't work on Terra anymore. I'd be happy to work with your team on another release.
This doesn't solve #88, but it might be a pathway to eventually getting to #82.
Successful run here. The commit says untested but it was tested upon push.