nf-core/proteinfamilies updates

Edit

This project aims to update the nf-core/proteinfamilies 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.

Update the update mechanism

Issue #122

Update the update mechanism of the pipeline to also output updated families .faa files, similarly to the basic execution mode.

Level: For anyone interested. Beginners welcome!

Update and add the trimal module to the pipeline

Issue #62

Update the trimal nf-core module and then use it in the nf-core/proteinfamilies pipeline. There can be two separate tasks that use this module:

1. As a clipkit alternative, to trim the gappy ends of multiple sequence alignments, that is also possibly faster (to benchmark).
2. As an alternative for the strict mmseqs clustering, for sequence similarity removal within families (to benchmark).

Level: For people with some experience in Nextflow/nf-core pipelines.