nf-core/genephylo

Path to comma-separated file containing information about the samples in the experiment.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Configure database option to either download a pre-formatted one (update), build a custom one (build) or reference a local database (current).

Path to a local database (required for current option).

Name of a ncbi pre-formatted nucleotide database (required for update option).

Path to the fasta file of the sequences for the custom database (required for build option).

Path to a file associating each sequence id of the custom database to its taxid (required for build option).

taxdump.tar.gz file containing nodes.dmp, names.dmp which assign taxonomy to NCBI taxIDs

choose either nucleotide or protein database

% of query vs hit identity

proportion of exact matches

number of hits with similiar or better score to by found by chance when searching the database of similiar size

positive matches to query sequence

numbers assigned by NCBI to identify taxonomical units

Choose which software to use to infer phylogenetic tree.

Species tree (Newick) used by Treerecs to reconcile the gene trees.

Display the help message.

Display the full detailed help message.

Display hidden parameters in the help message (only works when –help or –help_full are provided).

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