{
generic: 'MiGA: The Microbial Genomes Atlas',
quality_wf: 'Evaluate the quality of input genomes',
derep_wf: 'Dereplicate a collection of input genomes',
classify_wf: 'Classify input genomes against a reference database',
preproc_wf: 'Preprocess input genomes or metagenomes',
index_wf: 'Generate distance indexing of input genomes',
new: 'Create an empty MiGA project',
about: 'Display information about a MiGA project',
doctor: 'Perform consistency checks on a MiGA project',
browse: 'Explore a project locally using a web browser',
add: 'Create a dataset in a MiGA project',
get: 'Download a dataset from public databases into a MiGA project',
ncbi_get: 'Download the genomes of a taxon from NCBI to a MiGA project',
gtdb_get: 'Download the genomes of a taxon from GTDB to a MiGA project',
seqcode_get: 'Download all type genomes from SeqCode to a MiGA project',
rm: 'Remove a dataset from a MiGA project',
find: 'Find unregistered datasets based on result files',
ln: 'Link datasets (incl. results) from one project to another',
ls: 'List all registered datasets in a MiGA project',
archive: 'Generate a tar-ball with all files from select datasets',
add_result: 'Register a result',
stats: 'Extract statistics for the given result',
files: 'List registered files from a dataset or project',
run: 'Execute locally one step analysis producing the given result',
summary: 'Generate a summary table for the statistics of all datasets',
next_step: 'Return the next task to run in a dataset or project',
edit: 'Edit the metadata of a dataset or project',
option: 'Get or set options of a dataset or project',
touch: 'Change the "last modified" time to now without changes',
init: 'Initialize MiGA to process new projects',
daemon: 'Control the daemon of a MiGA project',
lair: 'Control groups of daemons for several MiGA projects',
db: 'Download a pre-indexed database',
date: 'Return the current date in standard MiGA format',
console: 'Open an IRB console with MiGA',
env: 'Shell code to load MiGA environment',
tax_set: 'Register taxonomic information for datasets',
tax_test: 'Return test of taxonomic distributions for query datasets',
tax_index: 'Create a taxonomy-indexed list of the datasets',
tax_dist: 'Estimate distributions of distance by taxonomy',
}
{
create_project: :new,
project_info: :about,
download: :db,
get_db: :db,
create_dataset: :add,
download_dataset: :get,
unlink_dataset: :rm,
find_datasets: :find,
import_datasets: :ln,
list_datasets: :ls,
result_stats: :stats,
list_files: :files,
run_local: :run,
sum_stats: :summary,
next_task: :next_step,
update_metadata: :edit,
c: :console,
add_taxonomy: :tax_set,
test_taxonomy: :tax_test,
index_taxonomy: :tax_index,
tax_distributions: :tax_dist,
}