Ampliseq Version 2.5.0

d4straub released this 02 Mar 18:34

· 911 commits to master since this release

78b7514

nf-core/ampliseq version 2.5.0 - 2023-03-02

Summary of changes

Added COIDB DADA2 taxonomic database
Small adjustments to taxonomic classification, ASV filtering by barrnap, fasta input
sbdi-export works for more taxonomic databases now
nf-core template update from 2.6 to 2.7.2

Detailed changes

`Added`

#518,#534 - Add COIDB DADA2 reference taxonomy database
#521 - Export svg in addition to pdf files for quality plots from DADA2
#538 - Parameter --diversity_rarefaction_depth controls the minimum rarefaction depth for diversity analysis, this allows increasing the rarefaction depth at the cost of excluding low count samples. Parameter --ancom_sample_min_count sets the minimum sample counts to retain a sample for ANCOM analysis.

`Changed`

#537 - Update output generated with option sbdi-export
#541 - Remove adjustments of taxonomic levels for RDP & SILVA & GTDB & UNITE database for DADA2 taxonomic classification, reduced default of --dada_tax_agglom_max from 7 to 6
#548 - --filter_ssu accepted any barrnap hit to a kingdom (domain) (any occurence in resulting gff) to choose an ASV, now only ASVs with the kingdom (domain) that has the lowest evalue are accepted.

`Fixed`

#513 - Template update for nf-core/tools version 2.7.2
#519 - Adding the pipeline reference to the MultiQC report
#520,#530 - Fix conda packages
#531,#546 - Update documentation
#535 - Make sure barrnap runs with fasta input
#544 - Adding module to fix header in fasta input if needed

`Dependencies`

#528 - Updated QIIME2

Tool	Previous version	New version
QIIME2	2022.8	2022.11

`Removed`

#513 - Removed parameter --enable_conda.

Assets 2