Latex & Markdown files

You have to use the option pipeTables:

\documentclass{article}
\usepackage[blankBeforeHeading, html, fencedCode,
            inlineFootnotes, citations, definitionLists,
            hashEnumerators, smartEllipses, hybrid, pipeTables]{markdown}

\usepackage{filecontents}
\begin{filecontents*}{\jobname.md}
This file is generated as a test for tables:

| Version | Date        |Paragraph| Description       | Author|
|:--------|:------------|---------|:------------------|-------|
| 1.0     | 12/Abril/19 | All     | initial commit    | RACG  |
| 1.0     | 12/Abril/19 | All     | initial commit    | RACG  |

\end{filecontents*}

\begin{document}
  \markdownInput{\jobname.md}
\end{document}

Maybe You should take a look at Pandoc: https://pandoc.org/ and convert .md files to LaTeX files?