1.5.0 - UNSC Punic

Added and Fixed

• Template update to 3.3.2.
• Addition of the --split_telomere boolean flag, this is false by default.
  • When true the pipeline will split the telomere file into a 5 and 3 prime file.
• Update ACCESSORY_FILES subworkflow:
  • Remove GET_LARGEST_SCAFFOLD as we no longer need it, this was needed for TABIX so that the correct index file was used. This was used by the TELO_FINDER and GAP_FINDER subworkflows.
• Update TELO_FINDER subworkflow:
  • Remove GAWK_MAP_TELO as it is no longer needed.
  • Remove GAWK_CLEAN_TELOMERE as it is no longer needed. The reason for its inclusion has been fixed.
  • Update EXTRACT_TELO to EXTRACT_TELOMERE which also removed the use of the cat {file} | awk pattern, replacing it with just awk. This was supposed to happen in 1.4.0, but was forgotten with the files lying dormant in the repo.
  • Refactor of the TELO_FINDER subworkflow, introducing the TELO_EXTRACTION subworkflow which is run per telo file. With the introduction of split_telomere this can be 3 files.
• Update LONGREAD_COVERAGE subworkflow:
  • Remove GRAPH_OVERALL_COVERAGE as it is not in use.
• Better formatting in some files.
• Moved GAWK_UPPER_SEQUENCE from the TELO_FINDER subworkflow to the first step of the main curationpretext workflow, this simply makes more sense.
• Removed no longer needed scripts from bin.
• Added the module GAWK_SPLIT_DIRECTIONS module, a local copy of the nf-core GAWK module.
• Added the gawk_split_directions.awk script for split telomere.
• Addition of GUNZIP for the input reference genome.
• Update tests.
• Added an "AUTO" value to the --aligner arg. If a genome is >5Gb it will use minimap2 else bwamem2.
• Parity update for the base.config to match TreeVal.
• Minor Doc updates.
• Comment out the CONDA workflow requirement, pipeline does not support conda.

Full Changelog: 1.4.2...1.5.0