MetaWorks v1.13.0

Added support for the mitochondrial 16S vertebrate classifier.

MetaWorks v1.12.0

Added support for the CUTADAPT '--rc' option to check the 5'->3' reads (default) and the reverse-complement for adapters/primers. In the conda environment, updated the following packages CUTADAPT 4.1 -> 4.2; VSEARCH 2.21.1 -> 2.22.1; SNAKEMAKE 7.12.1 -> 7.24.2 .

MetaWorks v1.11.3

Added library libuv to the conda environment to prevent an ORFfinder error on some systems.

MetaWorks v1.11.2

Added a compound grep search option to facilitate more complex taxon delimitation prior to pseudogene filtering to the ESV workflows.

MetaWorks v1.11.1

Updated snakefile_ESV to make pseudogene filtering quicker. This only affects cases where there are multiple groups being processed that each use different genetic codes, ex. vertebrates & invertebrates using COI.

MetaWorks v1.11.0

This version supports the production of two types of reports from the snakemake_ESV workflow: 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.

MetaWorks v1.10.0

Added support for the rbcL land plant classifier.

MetaWorks v1.9.6

Add the library libnghttp2 needed for ORFfinder to run on Centos7 on the GPSC. Updated README to provide instructions on how to update the LD_LIBRARY_PATH.

MetaWorks v1.9.5

Fixes a bug in the snakefile_OTU workflow and provides a new config_OTU.yaml . Instructions on how to run this workflow have been updated in the README.

MetaWorks v1.9.4

Fixed a bug in the dual-indexed snakemake pipeline to properly associate the dual-indexed tagged individual with the sample and amplicon info in the results.csv file. Does not affect any other snakemake dataflow.