Directories/restructuring #66
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The output directories have been updated but tests have not been. Additionally the output folder structure is modifiable within the modules.config file at the top level to fit in with the other pipelines, I think it is a cleaner way of specifying things as well. Tests have not been updated yet, however they will be after the module output names have been updated too reflect the process used to run them. As the tests will have to be updated twice otherwise. Additionally, the length filtered contigs are now set as the output contigs for follow up processes as they were not previously
Sadly while files are being renamed, some more tact was required in the process as I have inadverntly merged began oblititerating some outputs. The closure was updated to hopefully address this issue but more testing is needed
This is not a real commit, but the quast container is having issues running for some reason (once again with gridss). As the tests complete successfully in CI and the goal here to determine that the new outputs in some of the tests are coordinated we I just want to see what fails in github
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This PR has expanded in scope sadly (that is my fault). But the directories structure and naming of outputs has been updated along with the tests. Contigs that are filtered are now passed to other quality processes after filtering which addresses issue #55 and resulted in the addition of another parameter for skipping outputs. The IRIDANext config has been updated to reflect the updated output names and locations, however there is a chance that some outputs have been missed. |
apetkau
requested changes
Apr 24, 2024
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Thanks so much @mattheww95 for the amazing work you've put into this 😄 . A few comments.
changed output section and added TOC
emarinier
approved these changes
May 1, 2024
…kondo into directories/restructuring Merging upstream changes
…/restructuring Updating downstream branch from dev after patches applied for IRIDANext
…kondo into directories/restructuring merging upstream branch
apetkau
requested changes
May 6, 2024
Merged
apetkau
approved these changes
May 6, 2024
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Restruction of directories and outputs so that the outputs name conveys more meaning to users, and output tag types are added to file names.