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up: basecalling, nextflow.config, nextflow parameters and readability

João Henrique Chrusciel requested to merge dev/nxtcfg into main
  • Updated multiple variables in nextflow.config to match them across the different processes and workflows;
  • Added profiles in nextflow to facilitate the steps;
  • Added --kit-name configuration (params.barcoding_kit) to improve trimming during basecalling;
  • Changed descriptions across variables in nextflow.config;
  • Improved output directory name to include the projects' name (params.project_name);
  • Updated params.basecall_speed to use latest available simplex/modification model for basecalling;
  • Reorganized demux process to be included in the basecalling process to improve code readability;
  • Corrected few typos.

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