nextNEOpi_v1.3.0

This release comes with new features and improvements

Main changes:

• added epitope protein blast search:
  Predicted epitopes are now searched with blastp against UniProt and RefSeq protein databases for matches in non mutated protein sequences. Protein sequences that produced matches are indicated by their protein ID in the final neoantigen result tables.
• updated RIG score image/conda env
• updated nextNEOpi image/conda env to use GATK 4.2.5
• updated pVACtools image to pVACtools 3.0.0
  IEDB is now not included in the image and will be auto installed when running nextNEOpi
• updated NeoFuse image
• updated VEP to v105.0
• Breaking change: removed the options to pass input files via cmdline:
  All input files need to be passed via batch file
• Breaking change: format of the batch files changed to enable more flexibility in using mixed data (see README).
• enable NetMHCstab by default
  pVACseq 3.0.0. has standalone NetMHCstab

Improvements:

• nextNEOpi can now merge fastq files from multi lane runs into one fastq
• nextNEOpi can now use samples with SE and PE data mixed in a single batch file
• nextNEOpi can now use samples with RNAseq data and samples lacking RNAseq data in a single batch file
• improve publishDirMode
  introduce auto mode which defaults to link if hardlinks can be created, otherwise it is set to copy. If link is specified, we now check if hardlinks can be created, if not we set the mode to copy

Code cleanup:

• deprecated set changed to tuple
• use path instead of file for input: and output:
• remove TumorReplicateId and NormalReplicatId values from input/output and introduce a meta object which is passed on
• Simplify code by removing duplication of processes by leveraging the information passed in the meta object
• smarter handling of missing files by using lists