CWL workflow defintions for executing MGI analysis pipelines.
The master branch specifies DockerRequirement for each tool in the workflow.
By contrast, the toil_compatibility branch relies on large, a/k/a fat, Docker images. Below is a mapping of workflow to Docker image name, all available on DockerHub:
| Workflow | Docker Image | Main CWL |
|---|---|---|
| unaligned_bam_to_bqsr | mgibio/dna-alignment | unaligned_bam_to_bqsr/workflow.cwl |
| detect_variants | mgibio/cle | detect_variants/detect_variants.cwl |
| rnaseq | mgibio/rnaseq | rnaseq/workflow.cwl |
| tumor_only_exome | mgibio/cle | exome_workflow.cwl |
| umi_alignment | mgibio/dna-alignment | umi_alignment/duplex_workflow.cwl |
If a tool or workflow is a subworkflow of a larger workflow, then the same Docker image is required.
