Barbara Novak

This organism is still not in Ensemble, though a genome assembly has been deposited in GenBank (accession: GCA_039621445.1). Assembly fasta file is present, but the annotations are not available in...

**Workaround** Create a folder named `Metadata` inside the run folder and copy the runsheet into it. Ensure that the runsheet name matches the pattern `*_runsheet.csv`

**Workaround** Create a new reference table that lists the custom organism following the [pipeline description for generating [GeneLab Reference Annotations](https://github.com/nasa/GeneLab_Data_Processing/blob/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A.md)

Which version of the workflow are you running? Can you also provide information on the environment in which you ran the command? Was it a docker/singularity container (if so, which...

There is a typo in the NF_MGIllumina_1.0.0/envs/humann3.yaml file. The MetaPhlAn version should be `4.1.0` (as specified in the [GL-DPPD-7107-A](https://github.com/nasa/GeneLab_Data_Processing/blob/master/Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md) pipeline document) not `4.10` . An updated version of the environment...