Fix config outputs in workflow commands when set in config file

[JeanMainguy]

Summary

This PR addresses an issue with the default behavior of flat output file generation in workflow commands when specified through the configuration file.

Background

In the commands write_pangenome, write_genome, and draw, the default setting for output files is false, requiring users to explicitly specify the desired files via the command line. However, within workflow commands, these outputs are generated by default unless the --no_flat_files parameter is used. The intended behavior was to force output files to be generated by default unless overridden by the configuration file or CLI arguments.

Issue

The previous implementation incorrectly forced output file generation even when the configuration file specified false for certain outputs. This made it impossible to selectively generate some outputs while omitting others.

Fix

This PR corrects the handling of configuration and CLI arguments, ensuring that the specified settings in the configuration file are respected. Now, the correct outputs will be generated based on user specifications, allowing for more granular control over the output files.

Additional Fix

The compress flag, intended to compress output files, was previously not applied to the genomes_statistics.tsv file. This PR ensures that the file can now be generated in a compressed format if the compress flag is set.