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.