Workflow Types

Core Workflow Types

Title	Identifier	URL	# Workflows
Snakemake	https://doi.org/10.1093/bioinformatics/bts480	https://snakemake.readthedocs.io	21
Nextflow	https://www.nextflow.io/	https://www.nextflow.io/	41
KNIME	https://www.knime.com/	https://www.knime.com/	5
Galaxy	https://galaxyproject.org/	https://galaxyproject.org/	141
Common Workflow Language (CWL)	https://w3id.org/cwl/v1.0/	https://www.commonwl.org/	58

Title	Identifier	URL	# Workflows	Contributor
Jupyter	https://jupyter.org/	https://jupyter.org/	21	Douglas Lowe
Shell Script	Not specified	Not specified	11	Finn Bacall
PyCOMPSs	https://pypi.org/project/pycompss/	https://www.bsc.es/research-and-development/software-and-apps/software-list/comp-superscalar	8	Stian Soiland-Reyes
Scipion	Not specified	http://scipion.i2pc.es/	4	Stuart Owen
Janis	Not specified	https://janis.readthedocs.io/	1	Richard Lupat
Bpipe	Not specified	https://doc.bpipe.org	5	Sergi Sayols
Python	https://www.python.org/	https://www.python.org/	18	Genís Bayarri
Workflow Description Language (WDL)	https://doi.org/10.7490/f1000research.1114631.1	https://openwdl.org/	5	Finn Bacall
R Markdown document (RMD)	Not specified	Not specified	0	Adam Tofilski
R markdown (RMD)	Not specified	Not specified	1	Adam Tofilski
BioCompute Object (BCO)	https://doi.org/10.1109/IEEESTD.2020.9094416	https://biocomputeobject.org/	0	Stian Soiland-Reyes
Autosubmit (AS)	https://autosubmit.readthedocs.io/	https://autosubmit.readthedocs.io/	0	Bruno P. Kinoshita
MGnify Taxonomic profiling pipeline (motus_pipeline)	Not specified	Not specified	0	Ekaterina Sakharova
Pi	Not specified	Not specified	1	Tina Tian
Uniform Interface to Computing Resources (UNICORE)	Not specified	https://www.unicore.eu/	3	Thomas Gruber
Rbbt (Ruby bioinformatics toolkit)	Not specified	https://github.com/mikisvaz/rbbt-util	1	Miguel Vazquez