nextNEOpi_v1.4.1

This release contains some improvements and software updates

Updates

• GATK 4.5.0.0
• CNVkit 0.9.11
• BLAST 2.15
• multiqc 1.21
• pVACtools 4.1.1(fixes #43, #60, #66)
• VEP 111.0

Improvements

• remove sequenza from nextNEOpiENV and use it in separate ENVS
• switch from SGE to slurm in cluster profile example
• set process memory defaults for resource reservation to avoid OOM kills
• set default process time directive for max process execution time
• refine process CPU directive settings for
• changed the way how pvacseq results are concatenated. Now a python script using pandas is doing the job.

Fixes

• fix custom HLA file handling (fixes and closes #70, thanks to @mantczakaus)
• added custom HLA file example (closes #72)
• fix issued with pVACtools (#43, #60, #66)

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

nextNEOpi_v1.3.2b

This release contains bugfixes

Bugfixes

• fixed mixMHC2pred result parser. Closes #10
• fixed IEDB download. Prevent saving IEDB source tar.gz files with suffix after failed

nextNEOpi_v1.3.2a

This release contains a bugfix

Bugfix

• fixed incorrect MiXCR URL

nextNEOpi_v1.3.2

This release contains some improvements and software updates

Updates

• GATK 4.2.61
• pVACtools 3.0.2
• VEP 106.1
• MiXCR 4.0.0

Improvements

• fixed check for Mutect1
• added MiXCR licence check and installation, see README.md
• prevent unwanted $HOME bind mount to singularity containers
• pin to nextflow DSL to version 1

nextNEOpi_v1.3.1

This release contains bug fixes and updates

Fixes

• pipeline would fail when not trimming reads, due to non existing read channels
  reported by Xiaoke

• independent trimming of RNAseq or DNAseq reads only works correctly now

• updated NeoFuse image to include a race condition bug fix

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

nextNEOpi_v1.2.1

This release fixes issues encountered when running nextNEOpi with the conda profile (-profile conda)

Main changes:

• work around for incomplete GATK3 conda installation by downloading gatk3.8 jar and running gatk-register
• fix nextNEOpi conda yml file by setting pysam version 0.16
• use separate conda env for IGS
• check for correct conda channels when using conda profile
• reduce the default number of CPUs in conf/process.config example
• add tag in collectSampleInfo process
• doc: add a note about WGS data to README.md

Thanks to @aneichyk for reporting and testing.

nextNEOpi_v1.2

Changes:

• support BAM files as input data
• switch Singularity container repository from quay.io to https://depot.galaxyproject.org/singularity
• command line parameter to disable OptiType --disable_OptiType
• auto detection of PE/SE sequencing data
• deal with symlinked directories when using singularity
• do not auto bind mount the user home into singularity containers
• avoid race condition during ensembl VEP cache and plugin installation
• bug fixes
• updates: CNVkit 0.99, pVACseq 2.0.4
• code cleanup

nextNEOpi_v1.1

This is the first public nextNEOpi release