.. _automatic_report: Automatic Report **************** The :py:mod:`pyGenClean` module creates an automatic report using *LaTeX*. Each of the output directory will contain a final report (named ``automatic_report.tex``). The report, once compiled into the PDF format, includes various quality metrics. To compile the report, perform the following commands: .. code-block:: console $ pdflatex automatic_report.tex $ pdflatex automatic_report.tex $ pdflatex automatic_report.tex .. note:: Executing the command three times insure that the links in the automatic report are properly formed. Report merging ============== On a typical data clean up pipeline, multiple directories will be created (one for each of the parts of the pipeline). A script is provided to merge all those reports (one per ``data_clean_up.YYYY-MM-DD_HH.MM.SS`` directory) into a single report. Here is the usage of this script: .. code-block:: console $ pyGenClean_merge_reports --help usage: pyGenClean_merge_reports [-h] --qc-dir DIR [DIR ...] [--report-title TITLE] [--report-author AUTHOR] [--report-number NUMBER] [--report-background BACKGROUND] [--out-dir FILE] Merges automatic reports from other pyGenClean runs. optional arguments: -h, --help show this help message and exit Input: --qc-dir DIR [DIR ...] A list of directory containing pyGenClean runs. Report Options: --report-title TITLE The report title. [default: Genetic Data Clean Up] --report-author AUTHOR The current project number. [default: pyGenClean] --report-number NUMBER The current project author. [default: Simple Project] --report-background BACKGROUND Text of file containing the background section of the report. Output Directory: --out-dir FILE The name of the directory that will contain the final report. [default: pyGenClean_report] To execute the report merging procedure, perform the following command: .. code-block:: console $ pyGenClean_merge_reports --qc-dir data_clean_up.* .. note:: It is possible to change the title, the author, the number or the background of the automatic report by using the ``--report-title``, ``--report-author``, ``--report-number`` or ``--report-background`` options, respectively. Once again, to compile the final report, perform the following command: .. code-block:: console $ pdflatex pyGenClean_report.tex $ pdflatex pyGenClean_report.tex $ pdflatex pyGenClean_report.tex