Table 2.
Various types of workflow management systems are compared
| System | UI | Language | Application | Meta-info. | Reproducibility | Documentation |
|---|---|---|---|---|---|---|
| Galaxy | GUI | Python | Workflow editor | Generating | Workflow | Galaxy file (.ga) |
| Chipster | GUI | Java | Workflow view | None | Workflow | Chipster file (.bsh) |
| GeneProf | GUI | Java | Workflow designer | None | Workflow | Image file |
| GenePattern | GUI,CLI | Java | Additional module | None | Pipeline | GenePattern library |
| Taverna | GUI,CLI | Java,Scufl | Plugin | Three types | Workflow | Workflow file |
| TOGGLE | CLI | Perl | Text file | None | Perl script | Text file |
| bpipe | CLI | Goovy,Java | bpipe script | None | bpipe script | bpipe script |
| NGSANE | CLI | Bash | Text file | None | trigger.sh | Text file |
| nestly | CLI | Python | Python script | None | nestrun | Python script |
| Snakemake | CLI | Python | Build file | None | snakemake | Build file |
| Ruffus | CLI | Python | Python script | None | Python script | Python script |
| Makeflow | CLI | C | Makeflow Language | None | Makeflow script | Workflow script |
| SUSHI | GUI,CLI | Ruby | Ruby script | tsv format | Shell script | Shell script |
The systems are described by several features. The systems are categorized into two types by the user interface types, either GUI or CLI. Most systems have a proprietary format to save a workflow definition. More details are available in the Result section and in Additional file 7