Changelog
=========

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.