Cleaned repo, fixed installation issues with pip

Now this repo can be easily installed with pip install https://github.com/AntonelliLab/seqcap_processor/archive/refs/tags/v2.2.8.tar.gz, independent of conda. However, all dependencies need to be installed manually in that case. This is mostly a convenient way of updating secapr to the latest development version, from an existing conda environment where all dependencies are installed.

Fixed bugs in reference_assembly function

v2.2.7

fixed bug in reference_assembly

Fixed bug in clean_reads affecting files with short filenames

v2.2.6

bugfix clean_reads

Implementation of fastp, allows multiple fastq files (multiple runs) per sample

v2.2.5

mapping reads from multiple fastq files

Added cores flag to quality_check function

v2.2.4

added cores flag to quality_check function

Cleaned up repo

v2.2.3

cleaned up repo

Replaced pickle files with np.savetxt, bugfixes

v2.2.2

updated installation script

Bugfixes and more parallelization options

v2.2.1

small bugfixes

Small fixes

Fixed plot_sequences script and version of samtools dependency in recipe.

New align_sequences script

The align_sequences function is completely rewritten to majorly reduce the complexity of the code and take care of several dependency issues. New implementation of trimal for alignment trimming.