Changelog ========= Version 1.7-dev --------------- * Workflow modified to natively support RNA only patients (no SNV or InDels pMHCs will be reported). * Reimplemented support for intermediate file cleaning of trimmed FASTQs and BAMs (using ``raft.py run-workflow ... --clean-intermediates``). More information available in documentation and https://tinyurl.com/trick-nf-caching. * Reduced HLA allele consensus support requirement to single tool such that all alleles by all tools will be processed. Users can filter alleles (including by support) in the LENS report. * ``vcf2maf`` is run as part of workflow. * User-provided metadata files are automatically checked as part of ``raft.py run-ots`` and ``raft.py run-workflow`` modes. * Fixed bug preventing ``intersect`` variant combinging method from working. Version 1.6 ----------- * Fixed bugs within subjoin that prevented proper joining in some scenarios. * Added bed input file to mpileup\_parallel process for speed improvement. * Incorporated a manifest check within the LENS workflow that will terminate the workflow if an improper manifest is detected. * Added run-level suffix to some LENSTools outputs that did not already include it. * Improved split\_snaf\_by\_sample efficiency. * Standardized to BioContainers Docker images where possible. Users can expected further standardization using BioContainers in the future. * Updated HLA typing subworkflow to incorporate multiple HLA typers. * Removed alns\_to\_lens workflow until it can be properly integrated into the overall LENS workflow. * Updated somalier from 0.2.17 to 0.2.19. * Updated igv-reports from 1.8.0 to v.14.1. * Updated gtfparse from 1.0.1 to 1.0.7. * Updated cnvkit from 0.9.9 to 0.9.12. * Updated blast from 2.13.0 to 2.16.0 * Updated seqtk from 1.3 to 1.4. * Updated mhcflurry from 2.1.1 to 2.1.4 * Updated whatshap from 1.2.1 to 2.4. * Updated lenstools from 1.5.1 to 1.6. * Updated varscan from 2.1.1 to 2.4.6. * Updated deepvariant from 1.1.0 to 1.8.0. * Updated starfusion from 1.10.1 to 1.14.0. * Updated salmon from 1.1.0 to 1.10.3. * Updated gffread from 0.11.7 to 0.12.7. * Updated bedtools from 2.28.0 to 2.31.1 * Updated abra2 from 2.20 to 2.24. * Updated bcftools from 1.11 -> 1.21. * Updated gatk4 from 4.1.6.0 to 4.6.1.0. * Updated bowtie2 from 2.5.1 -> 2.5.4. * Updated minimap2 from 2.2.4 -> 2.28. * Updated bbmap from 38.86 to 39.17. * Updated bwa from 0.7.17 to 0.7.8. * Updated star from 2.7.0f to 2.7.3a * Updated fastp from 0.23.1 to 0.24.0. 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.