Release Ampliseq Version 2.7.0 · nf-core/ampliseq

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

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

#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

#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

#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