Research Object Crate for CWL4IncorporateTSSintoGXF (paired-end file)

[](./LICENSE)  [](https://www.docker.com/) [](https://bonohu.hiroshima-u.ac.jp/)   # 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](https://github.com/Linlab-slu/TSSr), is used to determine TSS. ## Requirements - [cwltool](https://github.com/common-workflow-language/cwltool) Install using pip ``` pip install cwltool ``` Install using conda ``` conda create -n cwltool conda activate cwltool conda install -c conda-forge cwltool ``` - [docker](https://www.docker.com/) † 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](https://github.com/RyoNozu/CWL4IncorporateTSSintoGXF/blob/main/config/workflow_template.yml) • Refer to the [Link](https://view.commonwl.org/workflows/github.com/RyoNozu/CWL4IncorporateTSSintoGXF/blob/main/workflow/cageseq_gtf_update_pe.cwl) 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](https://bioconductor.org/packages/release/bioc/html/BSgenomeForge.html) package ## Output files - updated gxf file (.gff/gtf) ## FYI: Running time ***

Author

Ryo Nozu, Sora Yonezawa

License

MIT

Contents