# Example CWL workflows for testing

## Whole Genome Sequencing - BWA + GATK 4.0 (with Metrics)

- [Reference](https://igor.sbgenomics.com/public/apps#admin/sbg-public-data/whole-genome-sequencing-bwa-gatk-4-0/)
- [JSON](https://igor.sbgenomics.com/raw/admin/sbg-public-data/whole-genome-sequencing-bwa-gatk-4-0/54)

## Whole Exome Sequencing - BWA + GATK 4.0 (with Metrics)

- [Reference](https://igor.sbgenomics.com/public/apps#admin/sbg-public-data/whole-exome-sequencing-bwa-gatk-4-0/)
- [JSON](https://igor.sbgenomics.com/raw/admin/sbg-public-data/whole-exome-sequencing-bwa-gatk-4-0/38)

## RNA-seq alignment - STAR 2.5.4b

- [Reference](https://igor.sbgenomics.com/public/apps#admin/sbg-public-data/rna-seq-alignment-star-2-5-4b/)
- [JSON](https://igor.sbgenomics.com/raw/admin/sbg-public-data/rna-seq-alignment-star-2-5-4b/19)

## RNA-seq - Salmon

- [Reference](https://igor.sbgenomics.com/public/apps#admin/sbg-public-data/salmon-workflow-0-9-1-cwl-1-0/)
- [JSON](https://igor.sbgenomics.com/raw/admin/sbg-public-data/salmon-workflow-0-9-1-cwl-1-0/20)
- [YAML](https://github.com/rabix/benten/blob/master/tests/cwl/sbg/salmon.cwl)

## Neoantigen workflow GATK 4.0

(Not included here for the 4MB file size)

- [Reference](https://igor.sbgenomics.com/u/vladimirk/neoantigen-workflow-demo/apps/#vladimirk/neoantigen-workflow-demo/nw)
- [JSON](https://igor.sbgenomics.com/raw/vladimirk/neoantigen-workflow-demo/nw/193)
