taxtriage
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jhuapl-bio
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-c...
## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...
### Description of feature Currently, you have to either pull (internet access required) taxa from NCBI post-kraken2, manually pull (also internet-requiring) AND/OR skip kraken2 and use a local reference FASTA...
### Description of the bug If a sample doesn't contain any trimmable reads, the file remains the same and the output is not emitted. This makes the pipeline fail. Make...
### Description of feature Currently, only Docker or Singularity are capable as profiles for launching the pipeline. Try to get conda up to date
### Description of the bug Currently, in singularity, Nanoplot fails when using longreads test file ### Command used and terminal output _No response_ ### Relevant files _No response_ ### System...
### Description of feature Adding 2 classifier approaches Centrifuge and metaPhlan2
### Description of the bug 1. E Coli really struggles in kraken2, and ultimately, it is a mess of 100s of strains being classified. Increasing how conservative the LCA mapping...
### Description of the bug Due to many metagenomic organisms not being found in HHS, a zscore of -1 (never present) dramatically increases reference size. For now, disable the -1...
### Description of feature - Enable fastq.gz files for all unaligned reads as an optional parameter: `save_unaligned`
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TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-c...