CWL4IncorporateTSSintoGXF

This workflow determines TSS based on the analysis of CAGE-seq data and incorporates TSS information and 5'UTR information calculated based on TSS information into the gene annotation file (gff/gtf). The R package, TSSr, is used to determine TSS.

Requirements

• cwltool

  Install using pip

  pip  install cwltool  
  

  Install using conda

  conda create -n cwltool  
  conda activate cwltool  
  conda install -c conda-forge cwltool 
  

• docker

  † and Docker Desktop must be running

Simple usage

• Clone this repository

  git clone https://github.com/RyoNozu/CWL4IncorporateTSSintoGXF.git
  cd CWL4IncorporateTSSintoGXF
  

• Run workflow

  # for paired-end reads case
  cwltool --debug --cachedir ./cwl_cache/ --outdir ./test/ ./workflow/cageseq_gtf_update_pe.cwl ./config/Workflow_config/cageseq_gtf_update_pe.yml
  

  • Prep your case yml file referring to the template
    • Refer to the Link for details on each parameter that needs to be specified
  • A single-ended version (cageseq_gtf_update_se.cwl) is in prep as of 20240417

Input files

• CAGE-seq Read (fastq, paried/single-end)
• reference genome (fasta)
• gene annotation file (gff/gtf)
• (BSgenome_data_package_seed_file (.txt))
  > refere to forgeBSgenomeDataPkg function in BSgenomeForge package

Output files

• updated gxf file (.gff/gtf)

FYI: Running time