message: docs: document outputs on failures
diff: @@ -105,6 +105,8 @@ Every row in tabular output corresponds to 1 input sequence. The meaning of colu
  | qc.stopCodons.status | Status for "Stop codons" QC rule |
  | isReverseComplement | Whether query sequences were transformed using reverse complement operation before alignment |
  | errors | List of errors during processing |
  +| warnings | List of warnings during processing |
  +| failedGenes | List of genes that failed translation |
  The table can contain additional columns for every clade-like attributes defined in reference tree in `meta.extensions.clade_node_attrs` and in the node attributes. For example, the default SARS-CoV-2 datasets define `Nextclade_pango` attribute which signifies a PANGO lineage assigned by Nextclade (see [Nextclade as pango lineage classifier: Methods and Validation](algorithm/nextclade-pango)).
  @@ -145,3 +147,19 @@ The file contains the following columns (delimited by commas):
  Nextclade CLI flag: `--output-errors`
  A table that, for each sequence, contains a list of warnings, errors as well as a list of genes affected by error. The genes listed in this table are omitted from translation, analysis and FASTA outputs.
  +
  +## Outputs for failed sequences
  +
  +When processing of a sequence fails for various reasons, not all output files will contain the corresponding entry (due to limitations of file formats):
  +
  +| Output file | CLI arg | Failed entries? |
  +|------------------------------|:------------------------|:-----------------|
  +| Aligned nucleotide sequences | `--output-fasta` | no |
  +| Aligned peptides | `--output-translations` | no |
  +| Auspice tree JSON | `--output-tree` | no |
  +| Analysis results CSV | `--output-csv` | yes |
  +| Analysis results TSV | `--output-tsv` | yes |
  +| Analysis results NDJSON | `--output-ndjson` | yes |
  +| Analysis results JSON | `--output-json` | yes |
  +| Insertions CSV | `--output-insertions` | yes |
  +| Errors CSV | `--output-errors` | yes |
  