Comments (12)
Ok thanks @Daniel-VM , I am now working on adding Flye, it's my first time contributing to nf-core, I was looking for guidance as waht is necessary to do.
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It would be great to have flye in here, but I do want to highlight that currently a template update would be really necessary.
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I'm on it, @d4straub! 👍🏾 I'm encountering a bit of trouble getting the latest template update to work in nf-core/bacass
.
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In addition, I would like to mention that we need to consider implementing Flye because it can already be accessed through the Dragonflye module, which is already implemented but in the development branch. I have to make a release ASAP 🏃🏾 .
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Awesome @lborcard. We have other interesting approaches in mind re: #57 . For example, improving assembled genomes by adding a genome rotation step. We proposed here cyclator or dnaapler or both.
Should we try them?
(Feel free to open a new issue to cover this genome rotation task 😃 )
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Awesome @lborcard. We have other interesting approaches in mind re: #57 . For example, improving assembled genomes by adding a genome rotation step. We proposed here cyclator or dnaapler or both.
Should we try them? (Feel free to open a new issue to cover this genome rotation task 😃 )
It seems that dnaapler is more recent and recently maintained but I don't have experience with either of these tools.
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So dnaapler/cyclator would take the output of Dragonflye? is there a module for either of these tools?
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Dragonflye is already present as module
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So dnaapler/cyclator would take the output of Dragonflye? is there a module for either of these tools?
I think so. I have never tryed yet, but it is likely that dnaapler takes the assembled genome *.fasta emmited by any assembler used in nf-core bacass (dragonflye, unicycler, miniasm, ...).
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I can work on a dnaapler module if that would help?
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Sure 💯 . Please add a git issue for dnaapler implementation ;).
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i added it to the list
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Related Issues (20)
- skewer.nf problem with Docker container. HOT 3
- Single end Illumina processing? HOT 1
- Working on updating the nf-core/tools template v2.9 HOT 2
- nf-validation on sample sheet HOT 3
- Released nf-core v2.10 template
- Enhance MultiQC to collect stats from all supported modules
- Removal of Prokka in favor of Bakta HOT 3
- New module - dragonflye - for long-read assembly
- Update bakta to v1.8.2
- Allow dragonflye to polish draft genome with short-reads
- Improvements in forked repository: KmerFinder, Estimation of Reference Genome, Custom Quast, and Custom MultiQC Reports HOT 3
- URGENT: pin nf-validation version HOT 2
- Fix warning messages on process name
- Save trimmed parameter saying 'false' is not a valid choice HOT 2
- Running error of exit status 255 HOT 1
- Prokka and Bakta are reporting single log in multiqc report when running multiple samples
- MultiQC Version 1.21 Parsing Issue
- Migration from nf-validation to nf-schema
- Chack whether `--assembly_type` parameter is requiered in nextflow run and update `README.md`
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