bacass
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nf-core
Simple bacterial assembly and annotation pipeline
### Description of feature I very much appreciate the functionality implemented with kmerfinder (that is automatic search for close genome and running Quast with it). However I'm running into several...
### Description of the bug Nanopolish doesn't run due to invalid input to MINIMAP2_POLISH step. ### Command used and terminal output ```consolenextflow run nf-core/bacass --input bso.tsv -profile docker --skip_kraken2 --assembler...
## PR checklist - [X] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add...
### Description of feature Allow `nf-core/bacass` to accept multiple FastQ files for the same sample and automatically concatenate them within the pipeline, eliminating the need for manual concatenation.
## PR checklist - [X] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add...
### Description of the bug ## Issue description The CAT_FASTQ process is not being used when the long-reads assembly mode is activated; it only currently works for short-read assemblies. This...
## PR checklist - [x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add...
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
## PR checklist - [x ] This comment contains a description of changes (with reason). - [ x] If you've fixed a bug or added code that should be tested,...
### Description of feature ## Description Add a post-assembly step to rotate circular bacterial chromosomes so that they start at the dnaA gene. This is useful for consistent genome comparisons...