Lili Andersson-Li

Hi, thanks for providing this very valuable resources. I am wondering why default `k-mer = 31 ` was not considered in kraken2 databases. To avoid high false positives? For Illumina...

Add the column db_type to database sheet

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Fix the issue https://github.com/nf-core/taxprofiler/issues/226 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code...

Simplify test profiles in CI test

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### Description of feature As pointed out by @maxulysse in #362, we should simplify the test profiles since the test is already included in the CI tests. Therefore should we...

### Description of feature Suggested by @maxulysse #362 Include all small files created by the taxprofiler pipeline in tower.yml.

Add porechop_abi to the pipeline

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Add `Porechop_ABI` to the pipeline as an alternative for adapter removal in long-read Oxford Nanopore data. Close the issue https://github.com/nf-core/taxprofiler/issues/145 ## PR checklist - [ ] This comment contains a...

Update modules

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Close https://github.com/nf-core/taxprofiler/issues/403 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

### Description of feature Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs / bins)...

### Description of feature Suggested by @jfy133 in [taxprofiler slack channel](https://nfcore.slack.com/archives/C031QH57DSS/p1719128116043699) [Lemur](https://github.com/treangenlab/lemur) is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets.

Overwrite the search patten of filtlong in multiqc_config.yml

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## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...