complete not supported yet?

[wwood]

(aviary-dev3)cl5n007:20220715:~/git/aviary$ aviary --help

                    ......:::::: AVIARY ::::::......

           A comprehensive metagenomics bioinformatics pipeline

Metagenome assembly, binning, and annotation:
        cluster   - Clusters samples based on OTU content using SingleM **TBC**
        assemble  - Perform hybrid assembly using short and long reads, 
                    or assembly using only short reads
        recover   - Recover MAGs from provided assembly using a variety 
                    of binning algorithms 
        annotate  - Annotate MAGs **TBC**
        genotype  - Perform strain level analysis of MAGs **TBC**
        complete  - Runs each stage of the pipeline: assemble, recover, 
                    annotate, genotype in that order.

Isolate assembly, binning, and annotation:
        isolate   - Perform isolate assembly **PARTIALLY COMPLETED**

Utility modules:
        configure - Set or overwrite the environment variables for future runs.

(aviary-dev3)cl5n007:20220715:~/git/aviary$ aviary complete --help
usage: aviary [--version] [--verbosity VERBOSITY] [--log LOG] {cluster,assemble,recover,annotate,genotype,viral,all,isolate,configure} ...
aviary: error: argument subparser_name: invalid choice: 'complete' (choose from 'cluster', 'assemble', 'recover', 'annotate', 'genotype', 'viral', 'all', 'isolate', 'configure')

[rhysnewell]

Ah yes, sorry complete should have a TBC and cluster should not have a TBC. I'll update this. If you want to run a pretty much full run, you can just use recover without providing an assembly and it will run everything except annotation and genotyping.

[wwood]

ah ok cheers

[rhysnewell]

Complete should now be supported as of latest commit to master