Release note 10.21.19

Recently published apps

Several new CWL1.0 apps have been published to the Public Apps Gallery:

New BROAD Best Practices workflows: Data Pre-processing and Germline snps and indels variant calling in version These workflows are built according to BROAD’s best practices following their WDL scripts, and together they allow for producing analysis-ready BAM files and VCF files with germline mutations.

eQTL analysis workflows: FastQTL and MatrixEQTL – Expression quantitative trait loci (eQTLs) are genomic variants related to variation in expression levels of mRNAs. These loci could be either cis, in the neighborhood of a gene transcription start site (TSS) or trans, distant eQTLs. The eQTL analysis workflow with FastQTL and MatrixEQTL are designed for fast eQTL analysis on large datasets, using standard mapping methods that test the linkage between variation in expression and genetic polymorphisms. FastQTL works with cis loci, while MatrixEQTL works with both cis and trans loci. These workflows are available on Cavatica, starting from standard bioinformatics file formats (VCFs and gene expression results), and producing a comprehensive set of plots, reports and results allowing for easier insight into eQTL analysis.

NanoStringQCPro 1.10.0: NanoString® has introduced the nCounter technology for direct counting of molecules in samples, which enables direct detection of specific RNA, DNA and protein molecules. It provides highly robust data across clinically relevant samples while reducing hands-on time and simplifying analysis. The NanoStringQCPro app performs basic QC steps and data normalization of NanoString mRNA gene expression data.