basic adaptations to work on FLI cluster as well

[johannesgeibel]

These changes were necessary to make the pipeline work on the FLI cluster. They included some adaptations to work on Slurm with Singularity containers (exporting of certain file systems and TMPDIR paths, queue naming) and setting file paths. Additionally, there remain some further questions before merging the branch:

• how to include additional clair 3 models in the best way
• Porechop_abi caused an error due to not renaming splitted reads correctly --> could be a problem of having methylation tags in the fastq. Still need to check and potentially open an issue for porechop_abi
• mosdepth curretly writes output to "Log" --> should write to "QC" instead?
• It would be helpful to add a final rule for multiqc to summarize QC results across samples
• setting of paths should be at the beginning of the "nextflow.config" file, as needs likely to be changed
• pipeline contains "meta/metadata_LR.csv", which needed to be renamed to "meta/LR_metadata.csv" --> should come from a parameter set in config instead
• for the BOV_LRC, certain participants might have their raw data as u.bam format --> should we provide a script to do bam to fastq transvertion, or include a process in pipeline?