Oncogenomics_NF_WF 5.1.1

Bug Fixes:

• Increase maxReadsInmemory for GATK step from 500000 to 1500000 by addind --maxReadsInMemory parameter. This helps pipeline from failing due to lack of memory for deep sequences samples.

##Chores/Misc:

• Update email recipients list for pipeline completion emails.
• Update pipeline version number.

Oncogenomics_NF_WF 5.1

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)

vPOC - version 5.0

POC working version. Works on:

• AWS AGC
• Biowulf