nf-core/ampliseq: Ampliseq Version 2.7.0

nf-core/ampliseq version 2.7.0 - 2023-10-20

Summary of changes

• Added Pipeline RMarkdown summary report
• Added optional ASV to OTU post-clustering with VSEARCH
• Added Kraken2 as another optional taxonomic classification tool
• Splitted --input into 3 parameters, --input now points to a sampleheet, alternatives are --input_fasta & --input_folder to accommodate nf-validation's fromSamplesheet
• Update to nf-core template to 2.10

Detailed changes

Added

• #558,#619,#625,#632,#644 - Pipeline summary report
• #615 - Phyloseq R object creation
• #622 - ASV post-clustering with Vsearch
• #637 - Taxonomic classification with Kraken2, parameter --kraken2_ref_taxonomy, --kraken2_ref_tax_custom, --kraken2_assign_taxlevels, --kraken2_confidence
• #639 - GTDB release 214.1 for taxonomic classification with DADA2, using --dada_ref_taxonomy gtdb or --dada_ref_taxonomy gtdb=R08-RS214
• #641 - Continue analysis even when individual files fail the filtering threshold, added parameter --ignore_failed_filtering

Changed

• #616 - When using a sample sheet with --input containing forward and reverse reads, specifying --single_end will only extract forward reads and treat the data as single ended instead of extracting forward and reverse reads.
• #616 - --input was split into three params: (1) --input for samplesheet, (2) --input_fasta for ASV/OTU fasta input, (3) --input_folder direct FASTQ input

| Param updated | Param old | Accepts | | ------------- | --------- | ---------------------------------------- | | input | input | samplesheet, .tsv/.csv/.yml/.yaml | | input_fasta | input | ASV/OTU sequences, .fasta | | input_folder | input | Folder containing compressed fastq files |

• #639 - --dada_ref_taxonomy gtdb points towards GTDB release 214.1 instead of GTDB release 207 for taxonomic classification with DADA2
• #645 - Updated documentation, including workflow figure

Fixed

• #605 - Make --sbdiexport compatible with PR2 version 5.0.0
• #614,#620,#642 - Template update for nf-core/tools version 2.10
• #617 - Fix database compatibility check for --sbdiexport
• #628 - Fix edge case for sample sheet input when using specific combinations of sampleID and forwardReads or reverseReads that will forward one file too much to cutadapt
• #630 - ASV rRNA (barrnap), length, and codon filter now work with ASV fasta file input
• #633 - UNIFRAC in QIIME2_DIVERSITY_CORE is now prevented from using a GPU to avoid errors
• #643 - Fix using --skip_dada_addspecies without --dada_ref_tax_custom_sp which was broken in 2.6.0 & 2.6.1
• #647 - Update of credits

Dependencies

• #646 - Updated dependencies, see below:

| software | previously | now | | -------- | ---------- | ------ | | FASTQC | 0.11.9 | 0.12.1 | | DADA2 | 1.22.0 | 1.28.0 | | PICRUSt2 | 2.5.0 | 2.5.2 | | QIIME2 | 2022.11 | 2023.7 |