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').

meaning we requested $cpus times as much as necessary.

':' caused Nextflow errors. E.g. 'arath:wg*' as output file to publishDir
would try to look for an 'arath' file.

Extract join_multiline from it.

- Finish climeMatrix and clime process
- Add gene set processes
- Use channel variables
- PhyML species as columns, CLIME species as row species
- clime-matrix accepts Orthogroups.txt instead of gene_families.tsv

Creates a gene sets file from gene_info.tsv and func_annot.csv.

Sometimes it worked without, sometimes it didn't, I suppose due to some
jobs running on the cluster which may reset the env and some locally
which apparently keep the env. It's no longer necessary to run nextflow
itself with the venv active.

Keep as species names, do not map to species objects. Make it easy to
map a name to a species obj anywhere.

Join removed as it's no longer used, use phase or cross in the future.
Plus, Nextflow has recently added a join operator of its own (not
equivalent).