bacass
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nf-core
Simple bacterial assembly and annotation pipeline
### Description of the bug When running the nf-core/bacass pipeline v2.4.0 with the required Nextflow version 24.04.2, a validation error occurs because the ID values in the samplesheet.csv file are...
### Description of the bug Hi there, When running bacass with miniasm set as the assembler using long reads only there is an pipeline stopping bug occurring in the racon...
### Description of the bug I am running into [this](https://github.com/rrwick/Unicycler/issues/221) issue with the Unicycler assembly step. It has apparently been fixed in 0.5.1, but I am using the 2.4.0dev version...
### Description of feature ## Description Implement a module for [dnaapler](https://github.com/kblin/dnaapler), a tool for rotating circular bacterial genomes to start at the dnaA gene. It’s a simpler alternative to Circlator,...
### Description of feature ## Description Update the pipeline to allow running multiple assemblers in parallel (e.g., Flye, MEGAHIT, Trycycler) followed by polishing, so users can compare results using tools...
### Description of feature ## Description Add a module for [gfastats](https://github.com/mdshw5/gfastats), a tool that parses assembly FASTA/GFA files and produces detailed metrics, including circularity status, which is helpful in bacterial...
### Description of feature ## Description Add a module for [Rasusa](https://github.com/mbhall88/rasusa), a tool for random downsampling of reads to a target genome coverage or number of bases. This can improve...
### Description of feature Add a module for [Circlator](https://github.com/sanger-pathogens/circlator), specifically the fixstart command, to reorient circular bacterial genomes to start at a standard gene like dnaA. Goal - Create a...
### Description of feature Some local modules are missing the `when `and `stub `sections, which are required to ensure proper functionality and compatibility with nf-core tests. Please review all local...
### Description of feature Some of the local modules lacks on meta.yml file: - [ ] modules/local/kraken2/db_preparation/meta.yml - [ ] modules/local/dfast/meta.yml - [ ] modules/local/kmerfinder/download_reference/meta.yml - [ ] modules/local/kmerfinder/kmerfinder/meta.yml -...