nextNEOpi_v1.5.1b

nextNEOpi_v1.5.1b

Version 1.5.1b-2025-06-05

• HLA Class II models
  Updated hlaii_models.txt, resolves #97 (initial comment in #64 )

nextNEOpi_v1.5.1a

Version 1.5.1a-2025-05-19

• sequenzaUtils
  Updates the singularity container URI for the sequenzaUtils label
  in the singularity profile. The new container uses a build based
  on Python 3.9 (py39he88f293) instead of Python 3.12 (py312h9c9b0c2).
  sequnza is not compatible with Python 3.12

• SequenzaUtils:

  • The seqz_binning window size (-w) is now conditional:
    • 50 if params.WES is true (for Whole Exome Sequencing).
    • 100 otherwise (for Whole Genome Sequencing).
      This solves potential memory issues with WGS data.

• Sequenza Process:

  • Sets the environment variable VROOM_CONNECTION_SIZE=10000000.
    This increases the connection limit for the vroom R package,
    helping to prevent errors when reading large seqz files.
  • The input gzipped seqz file (${seqz_file}) is now explicitly
    uncompressed to a temporary file (${seqz_file.getBaseName()})
    before being passed to SequenzaScript.R.
  • The temporary uncompressed file is removed after the R script
    completes.
    These changes aim to improve the stability and compatibility of
    the R script's file input handling.

nextNEOpi_v1.5.1

Version 1.5.1-2025-05-16

• GATK preprocessIntervalList:

  • Filters output of ScatterIntervalsByNs using awk to retain
    only canonical chromosomes (chr1-22, X, Y). This ensures
    downstream tools process relevant genomic regions and avoids
    potential issues with non-standard contigs.

• GATK SplitIntervals:

  • revert back --subdivision-mode from INTERVAL_SUBDIVISION to
    BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW.
    This mode aims for more even distribution of work across
    scattered jobs, potentially improving overall throughput,
    especially with unevenly sized intervals. It also avoids potential
    name collision due to splitting alignments across intervals

• GATK NVScoreVariants Threading Optimization:

  • Implemented dynamic configuration of threading environment variables
    to better utilize allocated CPUs:
    • OMP_NUM_THREADS, MKL_NUM_THREADS, OPENBLAS_NUM_THREADS
      are now set to task.cpus.
    • A new helper function getTFthreads(task.cpus) is introduced
      to intelligently set TF_NUM_INTRAOP_THREADS and
      TF_NUM_INTEROP_THREADS for optimized TensorFlow performance
      within NVScoreVariants.

• mixcr Process Memory:

  • Dynamically sets JAVA_Xmx (Java maximum heap size) based on
    task.memory.toGiga() for the mixcr process. This improves
    memory management and helps prevent potential out-of-memory errors.

Full Changelog: v1.5.0...v1.5.1

nextNEOpi_v1.5.0

Version 1.5.0 -2025-04-22

• Integrate Mosdepth for coverage calculation and reporting
• Parallelize GATK3 ReadBackedPhasing
• pVACsplice Integration:
  • Added regtools to identify splice junctions near variants.
  • Added infer_experiment and add_XS_tag for RNA strandness.
  • Integrated pVACsplice run and pvacsplice generate_protein_fasta.
  • Added new parameters (--pVACsplice_filter_set, etc.).
  • Updated pepChopper, mixMHC2pred, aggregated_reports, BLAST parsing, and output structure to handle splicing results.
• Dependency Updates:
  • GATK updated to 4.6.1.0.
  • pVACtools updated to 5.3.0 (includes mhcflurry downgrade to 2.0.6).
  • VEP updated to v113.
  • MiXCR updated to 4.7.0.
  • MixMHC2pred updated to 2.0.
  • IEDB MHCI updated to 3.1.6.
  • Major update of core Conda environment (Python 3.6 -> 3.10).
  • Updated various other tools (blast, cnvkit, multiqc, etc.).
  • Updated Gencode annotations to v47.
  • Updated base Singularity images.
• ASCAT Update: Replaced custom ASCAT 2.5 R scripts with ASCAT3 Conda package and process, using BAM inputs. Removed AlleleCounter and ConvertAlleleCounts.
• GATK: Renamed CNNScoreVariants to NVScoreVariants. Updated interval splitting parameters.
• Workflow & Script Refinements:
  • pepChopper.py now outputs context sequences to TSV.
  • Replaced HLAHD2mixMHC2pred.py with HLAHD2mixMHC2pred2.py.
  • Added gawk dependency.
  • Ensured tmpDir exists.
  • Fixed tabix index check in mutationalLoad.py.
  • Added tabix after NVScoreVariants.
  • Patched pVACtools BigMHC call.
• Configuration & Documentation:
  • Updated README (resource version, new params, output structure).
  • Updated parameters, process configs, and resource paths.
• Fixes:
  • #71, #82, #83, #90

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