Table 2 Various types of workflow management systems are compared
From: SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
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 |