Workflow Types

Core Workflow Types

Title Identifier URL # Workflows Contributor
Snakemake https://doi.org/10.1093/bioinformatics/bts480 https://snakemake.readthedocs.io 40
Nextflow Nextflow https://www.nextflow.io/ https://www.nextflow.io/ 59
KNIME https://www.knime.com/ https://www.knime.com/ 6
Galaxy https://galaxyproject.org/ https://galaxyproject.org/ 276
Common Workflow Language (CWL) https://w3id.org/cwl/v1.0/ https://www.commonwl.org/ 74

User-added Workflow Types

Title Identifier URL # Workflows Contributor
MGnify Taxonomic profiling pipeline MGnify Taxonomic profiling pipeline (motus_pipeline) Not specified Not specified 0 Ekaterina Sakharova
Docker Docker (Docker) https://www.docker.com/ https://www.docker.com/ 15 Genís Bayarri
Combine multi-wavelength workflows Not specified Not specified 0 Volodymyr Savchenko
Not specified Not specified 0 Rutger Vos
ONTViSc (ONT-based Viral Screening for Biosecurity) Not specified https://github.com/eresearchqut/ontvisc 0 Magdalena Antczak
Perl Not specified https://www.perl.org/ 1 Anand Maurya
ARA (Automated Record Analysis) Not specified https://github.com/maurya-anand/ARA 0 Anand Maurya
Integrating several EU-RI datasets with focus on preclinical and discovery research bioimaging Not specified Not specified 0 Elisabetta Spinazzola
Quarto Markdown Quarto Markdown (qmd) Not specified https://quarto.org/docs/authoring/markdown-basics.html 1 Stian Soiland-Reyes
Rbbt (Ruby bioinformatics toolkit) Not specified https://github.com/mikisvaz/rbbt-util 1 Miguel Vazquez
Uniform Interface to Computing Resources (UNICORE) Not specified https://www.unicore.eu/ 3 Thomas Gruber
Pi Not specified Not specified 1 Tina Tian
Jupyter https://jupyter.org/ https://jupyter.org/ 29 Douglas Lowe
Autosubmit Autosubmit (AS) https://autosubmit.readthedocs.io/ https://autosubmit.readthedocs.io/ 1 Bruno P. Kinoshita
BioCompute Object BioCompute Object (BCO) https://doi.org/10.1109/IEEESTD.2020.9094416 https://biocomputeobject.org/ 0 Stian Soiland-Reyes
R markdown (RMD) Not specified Not specified 4 Adam Tofilski
R Markdown document (RMD) Not specified Not specified 0 Adam Tofilski
Workflow Description Language (WDL) https://doi.org/10.7490/f1000research.1114631.1 https://openwdl.org/ 8 Finn Bacall
Python Python https://www.python.org/ https://www.python.org/ 34 Genís Bayarri
Bpipe Not specified https://doc.bpipe.org 5 Sergi Sayols
Janis Not specified https://janis.readthedocs.io/ 1 Richard Lupat
Scipion Not specified http://scipion.i2pc.es/ 7 Stuart Owen
COMPSs COMPSs http://compss.bsc.es/ http://compss.bsc.es/ 63 Stian Soiland-Reyes
Shell Script Not specified Not specified 13 Finn Bacall
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