There was a failure to install pyseqlogo from github.

See https://stackoverflow.com/q/71504533/1878788

Maybe it would be good to try other packages to plot logos (biotite ?).

This should be done via a "nodedup" switch in the pipeline config.

This resulted in a wrong symbolic link in the container.

Also made the genome preparation repository a submodule.

It has been generated using https://codemeta.github.io/codemeta-generator/, and is meant to help submission to Software Heritage.

This is part of an attempt to submit the code to Software Heritage
(https://www.softwareheritage.org/save-and-reference-research-software/)
to obtain a DOI for Eric Cornes' paper.

Function writing fastq was likely prematurely closing files due to wrong
sRNA name (tRF instead of tRFRNA).

Not tested yet.

Instead of installing them in the base container, they are installed
together with the workflows, using the versions from the requirements
file.

Cythonization failed due to lack of Cython, and versions were not the
same in requirements and bam25prime dependency.