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Tasks with hyphen in their name absent in workflow run results #103

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aniewielska opened this issue Jul 10, 2019 · 1 comment · Fixed by #188
Closed

Tasks with hyphen in their name absent in workflow run results #103

aniewielska opened this issue Jul 10, 2019 · 1 comment · Fixed by #188
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@stikos
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priority: medium Medium priority type: bug Something isn't working type flag: required by specs Compliance with specs requires this change workload: minutes Likely takes minutes to resolve

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@aniewielska
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That is another bug from a category "but you know it already".
For RD workflow (https://github.com/jarnolaitinen/RD_pipeline/blob/master/workflow.cwl)
some task names contain hyphens: gatk-ir, gatk-base_recalibration. Those tasks do not appear in the result of the run. That is because output parser only looks for words - which allows [a-zA-Z0-9_] and not a hyphen.
@uniqueg uniqueg added the bug label Sep 1, 2019
@uniqueg uniqueg removed the bug label Feb 20, 2020
@uniqueg
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uniqueg commented Apr 20, 2020 •
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Can be solved together with #128 and/or #152

@uniqueg uniqueg added priority: medium Medium priority type flag: required by specs Compliance with specs requires this change type: bug Something isn't working workload: minutes Likely takes minutes to resolve labels Apr 20, 2020
@stikos stikos self-assigned this Jun 12, 2020
stikos added a commit that referenced this issue Jun 12, 2020
@stikos
fix(logs): accept hyphens in task names
7fb5fa7 
Added the escaped hyphen character in the accepted characters group regex for task name retrieval

(#103)
@stikos stikos mentioned this issue Jun 12, 2020
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priority: medium Medium priority type: bug Something isn't working type flag: required by specs Compliance with specs requires this change workload: minutes Likely takes minutes to resolve
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fix: accept hyphens in task names elixir-cloud-aai/cwl-WES
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@uniqueg @stikos @aniewielska