Ampliseq Version 2.1.0 "Gray Steel Boa"

nf-core/ampliseq version 2.1.0 "Gray Steel Boa" - 2021-09-14

Summary of changes

• Updated documentation
• Added export to the Swedish Biodiversity Infrastructure (SBDI) on demand (--sbdiexport)
• Added newer versions of reference databases
• Predict community functions on demand (--picrust) for 16S rRNA amplicons with PICRUSt2
• Fixed some bugs

Detailed changes

Added

• #322 - Export to the Swedish Biodiversity Infrastructure (SBDI)
• #294 - New version of the PR2 taxonomy database: 4.14.0, contains also some Bacteria, see PR2 release 4.14.0 notes
• #294 - New version of the Unite taxonomy databases: 8.3
• #302 - Pipeline workflow figure in README.md
• #307 - Functional predictions with PICRUSt2, on demand with --picrust
• #310 - Workflow figure in usage.md when using --multiple_sequencing_runs
• #312 - Added curated GTDB 16S taxonomy: sbdi-gtdb as parameter to --dada_ref_taxonomy
• #318 - Output information about the used reference taxonomy in a separate file in results folder dada2/ or qiime2/taxonomy

Changed

• #313 - Relative abundance tables in qiime2/rel_abundance_tables/ on ASV level were renamed and with either DADA2 (rel-table-ASV_with-DADA2-tax.tsv) or QIIME2 classifications (rel-table-ASV_with-QIIME2-tax.tsv), if available.

Fixed

• #306 - Sample names can now be identical to basenames of read files
• #299, #301- Template update for nf-core/tools version 2.1
• #303 - Reverse primer of PacBio and IonTorrent reads should be now given to --RV_primer in usual direction (before: reverse complement)
• #305 - --max_len now accepts integers as expected
• #314, #315 - ASV fasta input via --input fixed (was broken in 2.0.0) and a test profile was added.

Dependencies

• #299 - Updated MultiQC to v1.10
• #319 - Updated DADA2 from 1.18.0 to 1.20.0