and:

- Mention count_groups.tsv in doc.
- Use snake case TSV headers instead.

- Split run_badirate and add to main.nf
- Various refactors

- Rename phylo_tree -> tree
- Remove unused fam_to_genes
- Derive fam_to_species_to_count where it's needed, locally

Refactors:

- Do use a dummy size file to be able to use -print_ids, but use a tmp file
  instead.
- ...

Changes:

- Do not write tree_ids.newick. If needed downstream, we'll write out a more
  convenient format.

Various refactors.

Changes:

- Create count_groups.tsv instead a gene_families.txt. Basically the
  same file as before minus the genes column as that can already be
  derived from the Orthogroups.txt file.
- Name groups deterministically. This will avoid cache misses in Nextflow.
- Do not write 0.txt. This was a fake input file used downstream to get
  list of species. Instead, one can get the species from a species file
  or as CLI args.

Refactors:

- Use parse.gene_families
- Use various.join_multiline
- Remove unnecessary list() conversion
- Click:
  - Disallow providing a dir to a file parameter and vice versa
  - Adjust help texts

Changes:

- Rename --phy-tree CLI param to --tree
- Crash when family gene missing from gene_info.txt instead of warning;
  it would be a bug.

- Rename variables: dir -> file for files, do not shadow builtins (e.g. dir)
- Refactor whitespace: Remove trailing whitespace, end files with 1 empty line, ...

Pulled commit f46756265e49e9a6e09777ea993a2618124e2663 from
https://gitlab.psb.ugent.be/deep_genome/pipeline_scripts/tree/master/

With the following changes:

- Remove IDE files (e.g. .idea), data files available online (e.g.
  gene ontology obo) and dependencies (e.g. BadiRate).

- Add copyright headers in lib/* dirs.

Main reason for merging into this repo without history instead of
keeping the scripts repo is that 1) the scripts repo was >2GB in size
due to inclusion of large data files, 2) most of the history was
uninformative (80% of the commit messages were 'V1').