qc

Configure the snippet manager, e.g. to set the security token from QOwnNotes

$ qc configure

$ qc search

$ qc exec --command

$ qc exec --command --last

$ qc switch

qc [OPTIONS] [FILES...]

--help, -h
    Displays a help message detailing the command's usage, available options, and arguments.

--version
    Shows version information for the specific qc implementation.

-o <dir>, --output-dir=<dir>
    Specifies the directory where output files, reports, or processed results should be generated. This is a common option for tools that produce new data.

-v, --verbose
    Increases the verbosity of the output, providing more detailed progress information, warnings, or debugging messages during execution.

--config <file>
    Specifies an external configuration file to load settings for the qc operation, allowing for flexible and reusable parameter sets.

--report-type <type>
    Defines the format of the generated report, such as HTML, JSON, TXT, or other specific formats. Only applicable if the qc command generates reports.

[FILES...]
    One or more input files to be processed by the qc command. These could be raw data files, results from previous steps, or configuration inputs.

The qc command is not a standard, universally installed Linux utility. Unlike core system commands like ls or grep, qc's presence and functionality are highly context-dependent and typically arise from specific software installations or custom user configurations.

Common contexts where a command named qc might be found include:
1. Bioinformatics: Often used as a shorthand or wrapper script for Quality Control (QC) procedures on biological data, especially high-throughput sequencing data. It might automate tasks performed by tools like FastQC or MultiQC, or perform custom data integrity checks.
2. Computational Chemistry/Physics: Within specialized software suites (e.g., Q-Chem, Gaussian, VASP), qc might refer to commands related to Quantum Chemistry calculations, such as job submission, post-processing of output files, or analysis of computational results.
3. Custom Scripts/Aliases: Many users or system administrators create an alias or a shell script named qc to encapsulate a series of frequently used quality checks, complex command pipelines, or specific data processing workflows tailored to their projects.

Due to its non-standard nature, the exact behavior, available options, and expected inputs/outputs of qc are entirely dependent on its specific implementation in the environment where it is encountered. Users should consult local documentation or script contents to understand its purpose.

The qc command is not a standard Linux utility and is not part of the core GNU or Unix toolset. Its presence and functionality are entirely dependent on specific software installations (e.g., bioinformatics tools, quantum chemistry packages) or custom user-defined scripts/aliases. Therefore, any analysis of qc must be context-specific. Users should consult the documentation pertinent to the software package or script where qc is used, as its behavior can vary widely.

When present, qc is commonly used for:
1. Preliminary Data Assessment: Quickly checking the quality and integrity of raw experimental data.
2. Automated Reporting: Generating summary reports that flag potential issues in data quality or computational output.
3. Job Management: In computational science, it might submit, monitor, or retrieve results from quantum chemistry calculations.
4. Workflow Integration: Serving as a modular component within larger data processing or computational pipelines.

Many users create their own qc alias or shell script. This allows them to quickly execute frequently used quality checks or complex command sequences with a simple, memorable command, tailoring it precisely to their specific project requirements or lab standards. These custom implementations are often found in a user's PATH via directories like ~/bin or as part of project-specific environment setups.

The 'history' of a command named qc is highly fragmented and specific to the domains in which it appears, rather than representing a unified lineage within general-purpose Linux. In bioinformatics, a qc utility typically emerged as a convenient wrapper or script to automate quality control workflows for high-throughput sequencing data, often to simplify complex command-line arguments or integrate multiple steps. Similarly, in computational chemistry, qc might be part of a larger software suite's user interface, developed to streamline the submission and analysis of quantum chemistry calculations. Its evolution is thus tied to the development and user convenience within these specialized scientific software fields, not a general operating system utility.

fastqc(1), multiqc(1), cutadapt(1), trimmomatic(1)