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”