Minor fixes

Updated pipeline to work with nextflow=24.10.0 and higher. Also added modules/pycistopic/module.config file to store the parameters of processes. Additionally updated README.md and example/ to make it easier to run pipeline

P.S. Now pipeline requires nextflow=24.10.0 or higher to run without problems

Metadata table and warnings

1. Added a step of metadata generation before the actual loading
2. ATAC data is now processed together with all other, so --atac flag was removed
3. Additionally a number of warnings (in case of some troubles) were added:

• warning when several .fastq files will have the same prefix after loading
• warning if total number of reads after cram to fastq conversion is not the same as in IRODS metadata
• warning when files of the same sample have inconsistent:
  • read length
  • library type
• warning if file is suspected to be 10X ATAC and is going to be renamed

23-310

Added an initial release after testing and finding issues so that nextflow can execute the repository remotely