New tree plot

[FernandoDuarteF]

No Issue associated to this PR.

Changes

1. Added a new tree plot method. Now both Quast and BUSCO outputs are plotted next to the tree.

• The script outputs the "complete" tree (BUSCO+Quast), the "complete no lenged" tree, only the tree, and only the legend, all in pdf format. Only the "complete" and the "complete no legend" trees are published in the results folder. Might be a good idea to also output separate plots for each BUSCO and Quast.

2. Changed the container for this plot, as new plotting method now requires ggtreeExtra from bioconductor.

Comments

For now the new container is in my quay.io repository, as I have not been able to push changes in our docker repository (see comment below).

There was a cropping issue related to Quast barplots in the new plotting method, I managed to fixed it using an extremely inelegant solution. It works, at least for now.

Perhaps a bin folder cleaning is necessary, but I left old scripts there for now.

[FernandoDuarteF]

This is the error message I get when trying to push changes in .github/workflows/push-genomeqc_tree.yml into the docker-build repository:

% git push origin new_genomeqc_tree
Enumerating objects: 13, done.
Counting objects: 100% (13/13), done.
Delta compression using up to 11 threads
Compressing objects: 100% (5/5), done.
Writing objects: 100% (7/7), 613 bytes | 613.00 KiB/s, done.
Total 7 (delta 4), reused 0 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (4/4), completed with 4 local objects.
To https://github.com/Eco-Flow/docker-build.git
 ! [remote rejected] new_genomeqc_tree -> new_genomeqc_tree (refusing to allow a Personal Access Token to create or update workflow `.github/workflows/push-genomeqc_tree.yml` without `workflow` scope)

[FernandoDuarteF]

I had to make changes in the gene_overlaps.R script so that genes with undefined strands ("." and "?") in the gff file are ignored.

It's impossbile to know in which strand these genes overlap with other genes, so they are not very informative in this context.

I'll open a new issue, as there might be a better way to tackle this.