nextNEOpi_v1.4.0

This release contains some improvements and software updates

Updates

• GATK 4.4.0.0
• pVACtools 4.0.1
• VEP 110.0
• MiXCR 4.4.1
• CNVkit 0.9.10
• IEDB mhcI 3.1.4
• IEDB mhcII 3.18
• NeoFuse (dev 202307) using Arriba v2.4.0

Improvements

• README contains now information about running the DSL1 pipelines with newer nextflow versions (closes #32)
• default cache policy is now lenient (closes #30)
• Better checking of resources files with better error handling (closes #36)
• added patch tool to rigscore image
• added the EL algorithms as default in pVACseq runs
• separated multiqc, fastp and fastqc from nextNEOpi env
• added a minimal test dataset (closes #33)

Fixes

• enable overwrites of timeline and report
• remove unused workDir parameter
• fix WGS scattering