The following apps were published in CWL1.x:
- Single Cell Multi Sample Pairwise Differential Expression Workflow - pipeline that performs differential expression analysis on single cell data between pairs of user defined conditions.
- Minimap2 v2.17 - a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database, tailored for use with long read sequencing technologies.
- fastqValidator 0.1.1 - checks format correctness of paired-end and single-end FASTQ files.
- FastP 0.20.1 - ultra-fast FASTQ preprocessor with useful quality control and data-filtering features, including adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of FASTQ data.
- SBG convert SRA/BAM to FASTQ - an all-in-one tool that converts SRA/SAM/BAM/CRAM files into FASTQ format.
- SBG Create Expression Matrix - creates aggregated matrices from various types of inputs, most typically from abundance estimates produced by tools like RSEM, Salmon, or Kallisto.
- SHAPEIT 4.2.1 - phasing tool for sequencing and SNP array data.
- Regenie 2.0.1 - tool for whole genome regression analysis.
- UMI-tools 1.1.1 - tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.