Comments (4)
fmalmeida
commented on May 26, 2024
The pb-assembly software is very difficult to implement in a pipeline since it possess a very specific configuration file that must be followed in order to execute it. And, it does not have a way to execute it in a command like manner, making it difficult to implement.
Its implementation would complicate a lot the execution of the pipeline making it almost impractical for people that are not bioinformatics experts.
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fmalmeida
commented on May 26, 2024
The same seems to happen with Nextdenovo
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fmalmeida
commented on May 26, 2024
Assemblers marked have been added! Execution tests are now being executed so the pipeline new version can be released.
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fmalmeida
commented on May 26, 2024
Assemblers added will be available in v2.3
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Related Issues (19)
- Improve quality assessment HOT 3
- Add option hifi
- Add an option for multiple samples HOT 9
- conda? HOT 11
- Shovill with all assemblers? HOT 2
- Add more parallel jobs HOT 1
- add polypolish tool HOT 1
- update documentation about the configuration in either config or samplesheet HOT 1
- Update CLI help message HOT 2
- change to unicycler v0.5.0? HOT 1
- new directory called "final_output"
- add testing git actions for PRs HOT 1
- use nf-core framework for CLI help and log messages HOT 3
- No valid choice in the pipeline parameters for hybrid strategies and problem with -c config HOT 9
- quast generating empty files HOT 24
- mkdir: cannot create directory HOT 4
- No such variable: USER HOT 11
- Include option for high quality long reads HOT 2
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