scanneo2 - ScanNeo v0.3.4

Fix

• Moved script for preparing hla input to workflow/scripts/genotyping
• Added missing pipe to log file in rule hlatyping_mhcII
• Added wrong input file to filtering of mhcII reads on SE

- Python
Published by riasc 11 months ago

scanneo2 - ScanNeo2 v0.3.3

### Fix

• Fixed parameter in .tests/integration/config_basic/config.yaml (align) to match general config

- Python
Published by riasc 11 months ago

scanneo2 - ScanNeo v0.3.2

Fix

• Removed fixed versions for bwa (0.7.19) and samtools (1.21) to allow installation of the latest versions.
• Updated the VEP wrapper version from "v1.31.1/bio/vep/annotate" to "v5.9.0/bio/vep/annotate".
• Modified functions for file type handling: adjusted indentation in getpreprocinput, updated getinputfilterreadsmhcIIPE to handle BAM files directly, renamed getalignedreads to getalignedreadsfeaturecounts, added new function getoutputhlatyping_mhcII, and updated rule input parameters accordingly.

- Python
Published by riasc 11 months ago

scanneo2 - ScanNeo v0.3.1

Fix

• Changed protocol for HLA alleles reference list to https (rule gethlainfo)
• Fixed path to input files in finalizemhcIIinput.py (which caused error when using paired-end reads)
• Fixed bug in quantification/featurecounts - supported regardless of input type (PE or SE): added wrapper script
• replaced MHC-II binding affinity prediction with IEDB API
• Manual Dockerfile replaces containerized version

- Python
Published by riasc 11 months ago

scanneo2 - ScanNeo2 v0.3.0

Features

• Added sequence similarity filter for MHC-I
  • self-similarity (using kernel similarity)
  • pathogen similarity (BLAST against pathogen-derived epitopes from IEDB)
  • proteome similarity (BLAST against human proteome)
• Prioritization of neoantigens is now done separately for each variant type (speeds up the process)
• Update to recent version of ScanExitron (Thanks to @dolittle007)
  • this version updated to recent version of regtools (v0.5.0) - which is available on Conda
  • Singularity/Docker is not necessary anymore
  • Added option to use strand information in exitron calling
• ScanNeo2 now uses conda environments for all tools (ditched Singularity/Docker)

Fix

• renamed similarity fields for pathogen and protein to more descriptive names

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.12

Fix

• Fixed missing alleles in HLA alleles reference list - #34

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.11

Fix

• Updated transindel environment to recent samtools version (as --o introduced in samtools >= 1.13 required by transindel)

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.10

Fix

• Force combining multiple VCF files in indel detection using mutect2 (e.g., when multiple samples are provided)

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.9

Fix

• Splitted rules in HLA typing to ensure better distribution of the workload
• Changed order in HLA typing rules (BAM files are now part of single-end)
  • samtools fastq is only called for BAM files
  • input of filtering directly from preprocessed/raw reads

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.8

Fix

• Added threads option to samtools sort calls to speed up the process
• Fixed wrong call to optitype within the wrapper script

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.7

Fix

• Separated samtools, bcftools and realign environments to avoid conflicts
• Changed order of genotyping rules to catch errors when no alleles can be found
  • Alleles are merged according to nartype (e.g., DNA, RNA) and then combined
• Force concat of VCF files in genotyping to avoid errors when no variants are found
• Added optitype wrapper to avoid errors when empty BAM files are provided / no HLA reads

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.6

Fix

• Added routines to catch errors when rnaseq data is not provided but exitron/alternative splicing calling is activated
• Added reference genome index as input to germline indel calling (necessary when only indel calling is activated)
• removed -C from BWA mem call (on DNAseq data) to avoid error on Illumina identifiers

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.5

Fix - Wrong indentation in HLAtyping caused error when providing no normal sample (NoneType was being iterated) - Fixed missing input in getreadshlatypingPE rule (tmp folder) that caused error when using paired-end reads - Added else case in getinputhlatyping function (rule getreadshlatypingPE) for input reads when preproc is deactivated

- Python
Published by riasc over 1 year ago

scanneo2 - ScanNeo2 v0.2.4

Fix

• Added concurrency to splAdder call
• Added routines that lets ScanNeo2 finish (even when splAdder results are empty or faulty)

- Python
Published by riasc almost 2 years ago

scanneo2 - ScanNeo2 v0.2.3

Features (somewhat)

• Added paramter nonchr in reference attribute to exclude non-chromosomal contigs from the reference genome

Fix

• Fixed wrong path in quality control for single-end reads

- Python
Published by riasc almost 2 years ago

scanneo2 - ScanNeo2 v0.2.2

Fix

• Updated spladder env to ensure that install wheel works (pysam requires python 3.6)

- Python
Published by riasc almost 2 years ago

scanneo2 - ScanNeo2 v0.2.1

Fix

• Removed hlahd path from config and hlatyping - needs to be installed in $PATH

- Python
Published by riasc almost 2 years ago

scanneo2 - ScanNeo2 v0.2.0

Features

• ScanNeo2 supports Snakmake>=8
  • --use-conda replaced by --software-deployment-method conda
  • --use-singularity replaced by --software-deployment-method apptainer
• Gather/scatter of the indel calling speeds up ScanNeo2 on multiple cores
  • added script to split bamfiles by chromosome (scripts/splitbamby_chr.py)
  • haplotypecaller first/final round is done per chromosome and later merged
  • mutect2 is done per chromosome and later merged
• Genotyping MHC-II works now on both single-end and paired-end
• User-defined HLA alleles are matched against the hla refset
• Added multiple routine to catch errors when only custom variants are provided
• Added additional parameters in config file

Fix

• When using BAMfiles the HLA typing wrongly expected single-end reads and performed preprocessing
• Each environment is no thoroughly versioned to ensure interoperability
• Missing immunogenicity calculation on certain values of MHC-I fixed
• Fixed prediction of binding affinity in MHC-II (as the columns are different from MHC-I)

- Python
Published by riasc almost 2 years ago

scanneo2 - ScanNeo2 v0.1.6

This release includes a small fix in which the prediction tools (e.g., binding affinity/immunogenicity) are additionally linked as input to the prioritization. This enables more flexibility in the order of the rules.

- Python
Published by riasc about 2 years ago

scanneo2 - ScanNeo2 v0.1.5

Small fix that replaces custom reference to global used ENSEMBL reference genome.

- Python
Published by riasc about 2 years ago

scanneo2 - ScanNeo2 v0.1.4

This release includes a small fix when snakemake first executed the exitron calling. The annotation was unavailable (as other rules had to be called first).

- Python
Published by riasc about 2 years ago

scanneo2 - ScanNeo2 v0.1.3

This release adds subroutines/fixes when no normal samples (in the config) are provided. ScanNeo used to abort when this is left empty due to a comparison with NoneType.

- Python
Published by riasc about 2 years ago