Changelog
=========


Version 1.5.1
-------------
* Fixed frameshift InDel peptide generation bug (where coding reading frame exceeds canonical stop codon).
* Changed to only use seq2HLA for HLA typing due to repeated Optitype failures.


Version 1.5
-----------------
* Added antitgen processing and presentation machinery (APPM) outputs to LENS report.
* Updated CTA peptide filtering such that peptides that occur in non-CTA transcripts are excluded.
* Updated LENS report to include all transcript ids, gene ids, and gene names that expressed peptide of interest.
* Added primary alignment RNA tumor read support for each pMHC. Note that all fusion-supporting RNA tumor reads are assumed to be primarily aligned.
* Include LENS version in output file name.
* Updated LENS workflow to support mouse samples.
* Updated LENS workflow to start from BAM files.
* Added LENS report to include column describing which variant callers detected SNV/InDel variants.
* Added LOHHLA output to LENS report.
* Added consensus-based approach to HLA typing.
* Updated HLA allele-specific expression to apply to consensus-based HLA calls.
* Added columns describing which HLA typers support each HLA allele.
* Added additional prioritization metrics to LENS reports.


Version 1.4
-----------------
* Fixed Resource allocations (defined in ``*.config`` files) to reduce cloud usage burden.
* Added gene signatures workflow (see ``gene_signatures`` module).
* Added gene signatures workflow dependencies (``binfotron``, ``tximport``, and ``generic``).
* Included ``set -o pipefail`` in ``bwa_mem2_samtools_sort`` process.
* Added HLA allele-specific expression (ASE) estimates in LENS report (requires ``seq2hla_ase`` call).
* Made HLA allele emission by ``seq2hla`` optional since sometimes ``seq2hla`` fails to identify alleles.
* Modified manifest parsing to allow for bypassing FASTQ symlinking (for AWS and GCP applications).
* Added QC analysis showing how filtering steps affect potential pMHC target removal (funneling).
* Included support for ``ar_``, ``nd_``, and ``ad_`` prefixes. Users are still encouraged to use the original prefix style.
* Modified MHCflurry process to allow 0 exit code if no HLA alleles present.
* Modified several ``neos`` module processes and workflows to allow emissions of outputs required for funneling analysis.
* Modified ``cnvkit`` workflow in ``onco`` module to use all normal DNA samples for guessing baits. Will be optimized in the future.
* Fixed ``bamblaster`` process call in ``samblaster`` to properly use provided CPUs and memory.
* Added ``seq2hla_ase`` process in ``seq2hla`` module.
* Added ``sequenza_merge_seqz`` label to ``merge_seqz`` process in ``sequenza`` module to allow proper resource allocation.
* Modified ``split_snaf_by_sample`` in ``snaf`` module to prevent non-zero exit if no sample-specific splice variants are detected.
* Added ``somatic_filter_parameter_dump`` process in ``somatic`` module to provide filtering information in SNV and InDel funneling plots.
* Modified ``tximport`` to fix transcript-to-gene raw counts for gene signatures workflow.
* Modified ``get_fastqs`` to allow copying (not symlinking) in AWS and GCP environments.
* Fixed ``varscan2_somatic_parallel`` workflow in ``varscan2`` module to fix InDel variant emission.
* Added labels to processes in ``viral`` module to ensure proper resource allocation.
* Added ``lohhla`` workflow to ``onco`` module to detect HLA loss of heterozygosity.
* Modified some processes (e.g. ``varscan2_somatic_by_chr``) to deal with tarball input files due to subdirectories not working properly in Google Cloud.a
* Modified ``tximport`` Docker image to support ``ps`` dependencies for Nextflow stats reporting.