Debian Science Project
Summary
Workflow
workflow management systems useful for scientific research

This task lists some packages providing workflow management systems useful for scientific research.

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Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Science to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Science mailing list

Links to other tasks
Index of all tasks

Debian Science Workflow packages

Official Debian packages with high relevance

capsule-nextflow
??? missing short description for package capsule-nextflow :-(
Versions of package capsule-nextflow
ReleaseVersionArchitectures
sid1.1.1+dfsg-1all
bookworm1.1.1+dfsg-1all
trixie1.1.1+dfsg-1all
forky1.1.1+dfsg-1all
Popcon: 18 users (106 upd.)*
Versions and Archs
 License: DFSG free
Git
coop-computing-tools
??? missing short description for package coop-computing-tools :-(
Maintainer: Alastair McKinstry
Versions of package coop-computing-tools
ReleaseVersionArchitectures
forky7.15.9-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid7.15.9-1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bookworm9.9-2amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
bullseye7.1.2-5amd64,arm64,armhf,i386
trixie7.14.5-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
Debtags of package coop-computing-tools:
uitoolkitncurses
Popcon: 33 users (105 upd.)*
Versions and Archs
 License: DFSG free
Git
cwltool
??? missing short description for package cwltool :-(
Versions of package cwltool
ReleaseVersionArchitectures
sid3.2.20260413085819-1all
forky3.2.20260413085819-1all
trixie3.1.20250110105449-3all
bookworm3.1.20230209161050-1all
bullseye3.0.20210124104916-3+deb11u1all
Popcon: 53 users (153 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reye, Bogdan Gavrilović, Carole Goble and The CWL Community: Methods included: standardizing computational reuse and portability with the Common Workflow Language. Communications of the ACM 65(6):54-63 (2022)
Registry entries: SciCrunch  Bioconda 
gearman
??? missing short description for package gearman :-(
Versions of package gearman
ReleaseVersionArchitectures
sid1.1.21+ds-1.1all
forky1.1.21+ds-1.1all
trixie1.1.21+ds-1all
bookworm1.1.20+ds-1all
bullseye1.1.19.1+ds-2all
upstream1.1.22
Debtags of package gearman:
rolemetapackage
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
gearman-tools
??? missing short description for package gearman-tools :-(
Versions of package gearman-tools
ReleaseVersionArchitectures
trixie1.1.21+ds-1amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
bullseye1.1.19.1+ds-2amd64,arm64,armhf,i386
bookworm1.1.20+ds-1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
forky1.1.21+ds-1.1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid1.1.21+ds-1.1amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
upstream1.1.22
Popcon: 26 users (122 upd.)*
Newer upstream!
 License: DFSG free
Git
make
??? missing short description for package make :-(
Maintainer: Stephen Kitt
Versions of package make
ReleaseVersionArchitectures
bookworm4.3-4.1amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x
trixie4.4.1-2amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x
forky4.4.1-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
sid4.4.1-3amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x
bullseye4.3-4.1amd64,arm64,armhf,i386
Debtags of package make:
develbuildtools
interfacecommandline
roleprogram
scopeutility
suitegnu
works-withsoftware:source
Popcon: 42322 users (13031 upd.)*
Versions and Archs
 License: DFSG free
Git
The package is enhanced by the following packages: make-doc
Screenshots of package make
python3-nipype
??? missing short description for package python3-nipype :-(
Versions of package python3-nipype
ReleaseVersionArchitectures
sid1.10.0-2all
trixie1.9.2-2all
bookworm1.8.5-3all
bullseye1.6.0-2all
upstream1.11.0
Popcon: 44 users (107 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza and KJ Millman: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools (eprint) 16th Annual Meeting of the Organization for Human Brain Mapping :106 (2010)
python3-wdlparse
??? missing short description for package python3-wdlparse :-(
Versions of package python3-wdlparse
ReleaseVersionArchitectures
forky0.1.0-3all
bookworm0.1.0-3all
sid0.1.0-3all
trixie0.1.0-3all
bullseye0.1.0-2all
Popcon: 12 users (121 upd.)*
Versions and Archs
 License: DFSG free
Git
snakemake
??? missing short description for package snakemake :-(
Versions of package snakemake
ReleaseVersionArchitectures
forky7.32.4-11all
bullseye5.24.1-2all
sid7.32.4-11all
bookworm7.21.0-1all
trixie7.32.4-7all
upstream9.21.0
Popcon: 48 users (135 upd.)*
Newer upstream!
 License: DFSG free
Git
Please cite: Johannes Köster and Sven Rahmann: Snakemake-a scalable bioinformatics workflow engine. Bioinformatics (2012)
Registry entries: Bio.tools  SciCrunch  Bioconda 
toil
??? missing short description for package toil :-(
Versions of package toil
ReleaseVersionArchitectures
forky9.3.0-3all
trixie8.0.0-5+deb13u1all
bookworm5.9.2-2+deb12u1all
sid9.4.1-1all
bullseye5.2.0-5all
Popcon: 38 users (133 upd.)*
Versions and Archs
 License: DFSG free
Git
Please cite: John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten: Toil enables reproducible, open source, big biomedical data analyses. Nature Biotechnology 35(4):314–316 (2017)
Registry entries: Bioconda 

Official Debian packages with lower relevance

cwlformat
??? missing short description for package cwlformat :-(
Versions of package cwlformat
ReleaseVersionArchitectures
sid2022.02.18-5all
bullseye2021.01.05-1all
forky2022.02.18-5all
bookworm2022.02.18-2all
trixie2022.02.18-3all
Popcon: 2 users (4 upd.)*
Versions and Archs
 License: DFSG free
Git
libbenchmark-tools
??? missing short description for package libbenchmark-tools :-(
Versions of package libbenchmark-tools
ReleaseVersionArchitectures
bookworm1.7.1-1all
trixie1.9.1-1all
experimental1.9.5-1~exp1all
sid1.9.1-1all
forky1.9.1-1all
bullseye1.5.2-2all
upstream1.9.5
Popcon: 0 users (0 upd.)*
Newer upstream!
 License: DFSG free
Git
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 284424