Skip to content

Oncogenomics_NF_WF 5.1
Compare
Choose a tag to compare
@vinegang vinegang released this 17 Sep 20:18
· 5 commits to main since this release
5.1
0f302da
This commit was created on github.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Learn about vigilant mode.

New Features/Enhancements:

  • Add Mantis to calculate MSI for tumor-normal pairs
  • Add Versions.yml to include version information for every tool used in the pipeline
  • Add Mouse workflow to perform mapping and rsem steps for downstream analysis.
  • Add Optitype and HLA-HD tools for HLAcalling.
  • Update command line in Read_depth and Coverage process. Add sort step for bed file and include -sorted option. This will reduce high memory usage for these processes.
  • Update bedtools command line. From bedtools 2.22.4 command line is reversed a=bed file and b=bam file
  • Update QC_stats_Final.py script python2 to 3 and add additional functionality to process hsmetrics file and extract values for mean bait coverage and mean target coverage.

Bug Fixes:

  • Update multiple_tumor and multiple_RNA workflows to handle variable no. of libraries per casename.
  • For deep sequenced files having a gz file as input for Sequenza process is causing memory errors on biowulf. Fix this by updating the input format.
  • Add "PASS" filter as criteria to filter variants from strelka2 output in vcf2txt.pl script.

Chores/Misc:

  • Remove deprecated code file Run_upto_quants.sh
  • Combine genotyping results and pipeline completed status emails into one email.
  • Add bco json and manifest json file generation for logs.
  • Create detailed documentation in git pages.
  • Remove platypus and freebayes code from vcf2txt.pl script - deprecated code.
  • Remove code for old HLAcalling tools(seq2HLA and HLAminer)
Assets 2
Loading