Overhauled workflow

[Shians]

• Simplified parameters and added validation via nf-schema
  • Multiple parameters renamed for clarity.
  • reads, read1, read2 have been replaced by fastq_r1 and fastq_r2.
  • R2_length argument removed, now directly calculated in workflow using fastq_r2.
  • genome_version argument now allows reference genome and annotations to be automatically downloaded. They can still be provided to overwrite via ref_fasta and ref_gtf. If overwritten, star_genome_index must also be provided.
  • Added --protocol argument to automatically set barcode inclusion list, umi length and barcode length.
• Changed dependency management to conda. Env file provided in env/pears_env.yml, used in all processes as declared in nextflow.config by process.conda.
  • Removed sub-modules in favour of management using conda.
• Restructured folders to better follow nextflow conventions. Runnable scripts moved to bin/ process components moved to modules/.
• Changed processes to follow proper Nextflow data pipelines, instead of reading and writing to paths outside of the working directory.
• Updated README to provide usage instructions.