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@nextstrain-bot nextstrain-bot released this 16 May 17:33
1.0.0-alpha.6
6053435

Nextclade CLI and Nextalign CLI

This version introduces verbosity levels for Nextclade CLI and Nextalign CLI.

The amount of information printed to console can now be changed using --verbosity flag. The following values are accepted (from least to most verbose):

  • silent
  • error
  • warn
  • info
  • debug

The default verbosity is warn.

Additionally, --silent flag is an alias for --verbosity=silent and --verbose is an alias for --verbosity=info.

The "silent" verbosity level guarantees that no console output is produced. This is handy when using stdout as output stream, e.g. with --output-fasta /dev/stdout, to avoid performance-costly file IO when "piping" output of Nextclade or Nextalign into the next stage of the processing pipeline which accepts inputs on stdin.

Additionally, the messages of warning verbosity (all warnings, including the ones produced when sequence alignment fails) are now being written to stderr instead of stdout.

Thanks @huddlej for the feature request.

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