summarize-rpbp-profile-construction#
Summarize the ORF profile creation step and prepare data for the web application.
usage: summarize-rpbp-profile-construction [-h] [-c] [--overwrite] [--tmp TMP]
[-p NUM_CPUS] [--log-file LOG_FILE]
[--enable-ext-logging]
[--log-stdout] [--no-log-stderr]
[--logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[--file-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[--stdout-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[--stderr-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
config
Positional Arguments#
- config
A YAML configuration file. The same used to run the pipeline.
Named Arguments#
- -c, --create-fastqc-reports
Create FastQC reports.
Default: False
- --overwrite
Overwrite existing output
Default: False
- --tmp
A temporary directory (FastQC).
- -p, --num-cpus
The number of CPUs to use.
Default: 1
logging options#
- --log-file
Log file (logging is redirected to this file, in addition to stdout and stderr, if specified).
Default: “”
- --enable-ext-logging
Enable logging for external programs that may be disabled by default, e.g. CmdStanPy.
Default: False
- --log-stdout
Log to stdout (in addition to a file and stderr, if specified).
Default: False
- --no-log-stderr
Do not send logging to stderr.
Default: False
- --logging-level
Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL
Logging level for all logs.
Default: “WARNING”
- --file-logging-level
Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL
Logging level for the log file. This option overrides
--logging-level
.Default: “NOTSET”
- --stdout-logging-level
Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL
Logging level for stdout. This option overrides
--logging-level
.Default: “NOTSET”
- --stderr-logging-level
Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL
Logging level for stderr. This option overrides
--logging-level
.Default: “NOTSET”