Updates the setup command implementation in commands/setup_cmd.py to set additional metadata items:
Default bases mask (extracted from RunInfo.xml), and
Flow cell mode (extracted from RunParameters.xml)
This requires that setup fetches copies of both these files to extract the information (previously only the sample sheet file was fetched).
The default bases mask is not used directly but may be helpful in cases when the bases mask needs to be modified when running the make_fastqs command (for example to trim one or more reads).
The flow cell mode was previously not set until make_fastqs had completed (this mechanism remains for now), however setting it on setup seems to make more sense.
Updates the
setupcommand implementation incommands/setup_cmd.pyto set additional metadata items:RunInfo.xml), andRunParameters.xml)This requires that
setupfetches copies of both these files to extract the information (previously only the sample sheet file was fetched).The default bases mask is not used directly but may be helpful in cases when the bases mask needs to be modified when running the
make_fastqscommand (for example to trim one or more reads).The flow cell mode was previously not set until
make_fastqshad completed (this mechanism remains for now), however setting it on setup seems to make more sense.