This project aims to update the nf-core/proteinannotator pipeline, by adding features described in the issues page.
Goal
Update the logic and add new features to the pipeline.
Tasks
See below a couple of potential new features to add during the hackathon. Depending on the participation and level of the attendees, more issues could be made available for the hackathon.
Incorporate the NMPFamsDB in the domain annotation subworkflow
Issue #77
Novel Metagenome Protein Families (NMPFamsDB) is a database which hosts novel metagenome protein clusters with no, or weak hits to Pfam or Reference genomes.
Use the HMM library from the resource, and search against it with hmmer/hmmsearch in the domain_annotation subworkflow, similarly to the existing Pfam and FunFam processes.
Level: For anyone interested. Beginners welcome!
Add nf-test and meta.yml files for the local functional_annotation subworkflow
Issue #78
The domain_annotation local subworkflow can be used as an example.
Level: For anyone interested. Beginners welcome!
Incorporate the eggnogmapper software in the functional annotation subworkflow
Issue #16
This should be done in two steps, similarly to interproscan;
first, download the required DBs, and second, run the eggnogmapper module.
The first task would be to update the existing nf-core/modules EGGNOGMAPPER module.
The next step would be to decide if it is better to create an nf-core module to download/preprocess the required databases, or re-use existing nf-core modules such as ARIA2 and UNTAR.
There is already an existing PR (#63) which can be salvaged for parts of the logic, or merge dev into that branch and continue from there.
Level: For people with some experience in Nextflow/nf-core pipelines.
