NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
This PR includes a new dockerfile for a more recent version of iqtree than is available as a biocontainer. Why? Because it seems that the seemingly random issue whereby some number of random species are dropped from starting trees, which leads to errors when running the module. Previously this would resolve itself by retrying those gene families (i.e. nextflow retry). Not a major issue, but if this happens enough, this becomes a non-negligible computational expense for no good reason.
This PR includes a new dockerfile for a more recent version of iqtree than is available as a biocontainer. Why? Because it seems that the seemingly random issue whereby some number of random species are dropped from starting trees, which leads to errors when running the module. Previously this would resolve itself by retrying those gene families (i.e. nextflow retry). Not a major issue, but if this happens enough, this becomes a non-negligible computational expense for no good reason.
The issue is described here: https://github.com/iqtree/iqtree2/issues/47 Existing but outdated containers for iq-tree are here: https://biocontainers.pro/tools/iqtree
Building the container unfortunately just takes a fair while - particularly when compiling the software.