Is there a way to skip outputs already generated in WDL?

Permanently deleted user

19 May 2023 00:00
2 comments

If you happen to know any tips on how to do that or know of resources that can hold the answer, I'll be very grateful with you!. I'm trying to generate a VCF QC for males/females within the X chromosome however there are some outputs that I've already generated that can be used for either of the 2 subsets and I do not want to generate them again. I'm using WDL workflow which consists of 3 main tasks. One of the tasks is the one that generates the output (bcftools leftnormalization) that can be use to subset either female or male individuals. How can I skip the generation of this output again in WDL? I have a lot of experience with SoS but I'm still a newbie for WDL. Thanks a lot for the help

Comments

2 comments

Ondrej Klempir DNAnexus Team
- 30 May 2023 09:26
1. An easy way would be to split/recompile your workflow into two workflows/apps, run the first just once and reuse the results later multiple times.
2. I would check the official supported features called "Smart reuse": https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-usage-and-storage-costs#smart-reuse-testing-workflows-efficiently-in-advance. From what I am reading here https://documentation.dnanexus.com/user/running-apps-and-workflows/job-reuse#enable-disable-smart-reuse about it, it seems that this should cover your use case well.
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Permanently deleted user
- 02 June 2023 17:52
Thank you. Smart Reuse was the key

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