message: docs: expand docs
diff: @@ -32,7 +32,7 @@ Nextclade expects the following input data:
  - (required) Reference phylogenetic tree, rooted at the reference (root) sequence.
  - CLI flag: `--input-root-sequence`
  + CLI flag: `--input-tree`
  It is used to assign clades and as a target for phylogenetic placement. The tree is expected to be sufficiently diverse and to meet clade assignment expectations of a particular use-case, study or experiment. Only clades present on the reference tree will be assigned. For more details see "Clade assignment" and "Phylogenetic placement" sections below).
  @@ -54,6 +54,14 @@ Nextclade expects the following input data:
  Accepted formats: [GFF3](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
  +- (required) Only in CLI. A subset of genes to use during analysis.
  +
  + Only these genes will be translated and only in these genes the aminoacid mutations will be detected.
  +
  + Accepted formats: comma-delimited list of gene names. All gene names in the list MUST be present in the gene map (see `--input-gene-map`).
  +
  + CLI flag: `--genes`
  +
  - (optional) Table of PCR primers - a table that describes a set of PCR primers that might be used for PCR tests of the virus.
  CLI flag: `--input-pcr-primers`
  