terrimporter/MetaWorks: MetaWorks v1.11.0

This version supports the production of two types of reports: 1) the original report.csv that combines the ESV.table, taxonomic assignments, and sequences into a single CSV file, and 2) separate files for ESV.table, taxonomic assignments, and sequences (denoised sequences/ORFs/trimmed ITS) each indexed by the same global ESV ids. Report type 1 is appropriate for users with 10s to low 100s of samples because this is a memory-intensive step. Report type 2 is more appropriate for users with high 100s of samples or greater.

The MetaWorks_v1.11.0 environment now uses newer versions of underlying software: snakemake 6.7.0 -> 7.12.1, cutadapt 3.4 -> 4.1, and vsearch 2.18.0 -> 2.21.1. In cutadapt, we include the --fasta parameter to force FASTA formatted output. In vsearch, the dereplication step used to use derep_fulllength but that function has been deprecated so now we use the fastx_uniques function with the fastaout parameter.