nf-core/ampliseq: Ampliseq Version 2.3.0

nf-core/ampliseq version 2.3.0 - 2022-04-04 Summary of changes

• Added Barrnap that annotates whether ASV sequences are SSUs and filter on demand
• Primer sequences are now not required any more and cutadapt can be skipped
• Updated to nf-core template 2.3.2
• Fixed some bugs

• #385 - --skip_cutadapt allows to skip primer trimmimg.
• #390, #408 - Add values to option --cut_its, specifying which ITS part to use. Also, add option --its_partial <x> to allow partial ITS sequences longer than given cutoff.
• #395 - --seed specifies the random seed.
• #396 - Barrnap annotates ASV sequences for SSU's, it can be skipped with --skip_barrnap. --filter_ssu takes a comma separated list of "bac,arc,mito,euk" and enables SSU filtering depending on Barrnap (default: off).
• #397 - Complement README.md with links to the nf-core bytesize 25 (nf-core/ampliseq).

• #385 - --FW_primer and --RV_primer are not obligatory any more, however primer sequences are still required with cutadapt (i.e. without --skip_cutadapt), --qiime_ref_taxonomy, and --cut_dada_ref_taxonomy (cuts reference with primer sequences).

• #384 - For QIIME2 beta diversity, make directory before execution.
• #394 - Prevent simultaneous usage of --qiime_ref_taxonomy and --classifier.
• #402, #410 - Template update for nf-core/tools version 2.3.2
• #403 - Limit number of files for DADA2_QUALITY (plotQualityProfile) by read numbers.
• #405 - Fix omitting taxonomic filtering (QIIME2_FILTERTAXA).
• #404 - Rephrase error message for empty input files and empty files after trimming with cutadapt.
• #407 - Fix reformatting script for Unite.