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.