Improve help messages (#30)

* Better detection of fastq files

* Fix bug when directory does not exist

* Improve robustness and logging of fastqimporter

* Remove unnecessary cast

* Split merged parameters in bowtie2

* Remove poetry.lock from index

* Reindex poetry.lock

* Reduce memory usage in counter

* Improve help

* No filtering according to core and changed message for gene merging.

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Co-authored-by: Florian Plaza Onate <[email protected]>