nextstrain/nextclade

`--input-pcr-primers` listed in CLI help options despite being removed in v3

kapsakcj opened this issue · 2 comments

kapsakcj commented

Just want to report that the --input-pcr-primers option for nextclade run is listed in the help options. According to migration docs here: https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html#some-cli-arguments-for-individual-input-files-are-removed this option has been removed.

Is it still available as an option? or perhaps just an oversight on the CLI help options?

I don't need to use this option, just wanted to let you know.

to reproduce:

$ docker run --rm nextstrain/nextclade:3.3.1 nextclade run --help | grep -A 4 'pcr-primers'
      --input-pcr-primers <INPUT_PCR_PRIMERS>
          Path to a CSV file containing a list of custom PCR primer sites. This information is used to report mutations in these sites.
          
          Supports the following compression formats: "gz", "bz2", "xz", "zstd". Use "-" to read uncompressed data from standard input (stdin).
ivan-aksamentov commented

@kapsakcj Hi Curtis,

Indeed. The functionality has been partially restored in 3.1.0 (#1398) due to popular demand (#1388). The docs need to be fixed.

kapsakcj commented

Ah ok, thanks for the explanation.