Repo for building an interactive workbench for scRNA analysis. The interactive workbench is built with Open OnDemand service. The analysis are performed with cellranger pipeline and scanpy.

• Jobwrappers (contains job wraper script to run cellranger and jupyter scanpy notebook)

  • cellranger_aggr.sh
  • cellranger_bcl2count.sh
  • cellranger_mkfastq.sh
  • scanpy-scrna-analysis.ipynb

• OOD_app (OOD app that presents three web forms on the dashboard)

  • cellranger_aggr
  • cellranger_bcl2count
  • cellranger_bcl2fastq

============================================

List of Scientific Workflow Management Systems

============================================

See here: https://github.com/pditommaso/awesome-pipeline, https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems

• Apache Airflow https://github.com/apache/airflow
• NextFlow http://nextflow.io
• Makeflow http://ccl.cse.nd.edu/software/makeflow/
• Pyflow https://github.com/Illumina/pyflow
• Cluster Flow http://clusterflow.io
• Pegasus http://pegasus.isi.edu/
• Parsl (a Parallel Scripting Library for Python) http://parsl-project.org
• Swift & Swift/T http://swift-lang.org/main/ http://swift-lang.org/Swift-T/
• Galaxy http://galaxyproject.org/
• Apache Taverna http://www.taverna.org.uk/ https://taverna.incubator.apache.org/
• Kepler https://kepler-project.org/
• flowr (R-based) http://docs.flowr.space/ https://github.com/sahilseth/flowr
• Arvados - CWL-based distributed computing platform for data analysis on massive data sets.https://arvados.org/ https://github.com/arvados/arvados
• SHIWA https://www.shiwa-workflow.eu/
• Apache Oozie https://oozie.apache.org/
• DNANexus https://wiki.dnanexus.com/API-Specification-v1.0.0/IO-and-Run-Specifications https://wiki.dnanexus.com/API-Specification-v1.0.0/Workflows-and-Analyses
• Agave http://agaveapi.co/live-docs/
• DiscoveryEnvironment http://www.iplantcollaborative.org/ci/discovery-environment
• Wings http://www.wings-workflows.org/
• Knime https://www.knime.org/
• Snakemake https://github.com/snakemake/snakemake https://snakemake.readthedocs.io/en/stable/
• BPipe http://bpipe.org http://docs.bpipe.org/
• Ruffus https://code.google.com/p/ruffus/
• Luigi http://github.com/spotify/luigi https://luigi.readthedocs.io
• SciLuigi. Helper library built on top of Luigi to ease development of Scientific workflows in Luigi: http://github.com/pharmbio/sciluigi
• Luigi Analysis Workflow (LAW) https://github.com/riga/law
• GATK Queue https://www.broadinstitute.org/gatk/guide/topic?name=queue
• Yabi https://ccg.murdoch.edu.au/yabi
• Ketrew https://github.com/hammerlab/ketrew
• Cosmos https://cosmos.hms.harvard.edu/documentation/index.html http://bioinformatics.oxfordjournals.org/content/early/2014/07/24/bioinformatics.btu385.full [paper] Cosmos2: https://github.com/LPM-HMS/COSMOS2 http://cosmos.hms.harvard.edu/COSMOS2/
• Pinball https://github.com/pinterest/pinball
• bcbio https://bcbio-nextgen.readthedocs.org/en/latest/
• Chronos https://github.com/mesos/chronos
• Azkaban https://azkaban.github.io/
• Apache NiFi https://nifi.apache.org/docs/nifi-docs/html/overview.html
• Mistral https://github.com/arteria-project https://wiki.openstack.org/wiki/Mistral#What_is_Mistral.3F https://docs.openstack.org/mistral/latest/user/wf_lang_v2.html
• nipype http://nipy.org/nipype/
• End of Day https://github.com/joestubbs/endofday
• BioDSL https://github.com/maasha/BioDSL
• BigDataScript http://pcingola.github.io/BigDataScript/
• Omics Pipe: uses Ruffus http://sulab.scripps.edu/omicspipe/
• Ensembl Hive https://github.com/Ensembl/ensembl-hive
• QuickNGS http://bifacility.uni-koeln.de/quickngs/web
• GenePattern http://www.broadinstitute.org/cancer/software/genepattern/
• Chipster http://chipster.csc.fi/
• The Genome Modeling System https://github.com/genome/gms
• Cuneiform, A Functional Workflow Language https://github.com/joergen7/cuneiform http://www.cuneiform-lang.org/
• Anvaya http://www.ncbi.nlm.nih.gov/pubmed/22809419 http://webapp.cabgrid.res.in/biocomp/Anvaya/ANVAYA_Main.html#HOWTO_INSTALL_ANVAYA
• Apache Airavata http://airavata.apache.org/
• Unipro UGENE http://ugene.net/ https://doi.org/10.7717/peerj.644
• CloudSlang http://www.cloudslang.io/
• Stacks http://catchenlab.life.illinois.edu/stacks/
• Leaf http://www.francesconapolitano.it/leaf/index.html
• omictools http://omictools.com/
• YAWL yet another workflow language https://doi.org/10.1016/j.is.2004.02.002 http://www.yawlfoundation.org/
• Triquetrum https://projects.eclipse.org/projects/technology.triquetrum https://github.com/eclipse/triquetrum/
• Kronos https://github.com/jtaghiyar/kronos
• qsubsec https://github.com/alastair-droop/qsubsec https://doi.org/10.1093/bioinformatics/btv698
• YesWorkflow http://yesworkflow.org
• gwf - Grid WorkFlow https://github.com/gwforg/gwf http://gwf.readthedocs.io/
• Fireworks. https://pythonhosted.org/FireWorks/
• NGLess: NGS with less work http://ngless.rtfd.io
• pypipegraph https://github.com/TyberiusPrime/pypipegraph
• Cromwell https://github.com/broadinstitute/cromwell
• Dagobah - Simple DAG-based job scheduler in Python. https://github.com/thieman/dagobah
• sushi https://github.com/uzh/sushi
• Clinical Trial Processor - A program for processing clinical trials data. http://mircwiki.rsna.org/index.php?title=MIRC_CTP
• Noodles http://nlesc.github.io/noodles/
• Consonance (runs SeqWare & CWL) https://github.com/Consonance/consonance/wiki
• Dog https://github.com/dogtools/dog
• Produce https://github.com/texttheater/produce
• LONI Pipeline http://pipeline.loni.usc.edu/
• Cpipe https://github.com/MelbourneGenomics/cpipe
• AWE https://github.com/MG-RAST/AWE
• (Py)COMPSs https://www.bsc.es/research-and-development/software-and-apps/software-list/comp-superscalar/
• KLIKO https://github.com/gijzelaerr/kliko
• SoS Workflow https://github.com/vatlab/SoS https://vatlab.github.io/sos-docs/ https://doi.org/10.1093/bioinformatics/bty405 https://doi.org/10.1371/journal.pcbi.1006843
• XNAT Pipeline Engine https://wiki.xnat.org/display/XNAT/Pipeline Engine https://wiki.xnat.org/display/XNAT/XNAT Pipeline Development Schema
• Metapipe https://github.com/TorkamaniLab/metapipe
• OCCAM (Open Curation for Computer Architecture Modeling) https://occam.cs.pitt.edu/
• Copernicus http://www.copernicus-computing.org
• VisTrails https://www.vistrails.org
• Dagman A meta-scheduler for HTCondor https://research.cs.wisc.edu/htcondor/dagman/dagman.html
• UNICORE https://www.unicore.eu/docstore/workflow-7.6.0/workflow-manual.html#wf_dialect
• Toil (A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python) https://github.com/BD2KGenomics/toil
• Civet https://github.com/TheJacksonLaboratory/civet
• Cumulus https://github.com/Kitware/cumulus
• High-performance integrated virtual environment (HIVE) https://hive.biochemistry.gwu.edu
• Cloudgene http://cloudgene.uibk.ac.at/cloudgene-yaml
• FASTR https://bitbucket.org/bigr_erasmusmc/fastr/ http://fastr.readthedocs.io/en/stable/
• BioMake https://github.com/evoldoers/biomake https://doi.org/10.1101/093245
• remake https://github.com/richfitz/remake
• SciFloware http://www-sop.inria.fr/members/Didier.Parigot/pmwiki/Scifloware/
• OpenAlea http://openalea.gforge.inria.fr/dokuwiki/doku.php https://hal.archives-ouvertes.fr/hal-01166298/file/openalea-PradalCohen-Boulakia.pdf
• COMBUSTI/O https://github.com/jarlebass/combustio http://hdl.handle.net/10037/9361
• BioCloud https://github.com/ccwang002/biocloud-server-kai https://doi.org/10.6342/NTU201601295
• |ss| Triana http://www.trianacode.org/ |se| (website seems to have been taken over by SEO)
• Anduril http://anduril.org/site/
• dgsh http://www.dmst.aueb.gr/dds/sw/dgsh/
• EDGE bioinformatics: Empowering the Development of Genomics Expertise https://bioedge.lanl.gov/edge_ui/ http://edge.readthedocs.io/ https://lanl-bioinformatics.github.io/EDGE/
• Pachyderm http://pachyderm.io/ http://pachyderm.readthedocs.io/en/stable/advanced/advanced.html
• Digdag https://www.digdag.io/
• Agua / Automated Genomics Utilities Agent http://aguadev.org
• BioDepot Workflow Builder (BwB) https://github.com/BioDepot/BioDepot-workflow-builder https://doi.org/10.1101/099010
• IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses http://r3lab.uni.lu/web/imp/ https://doi.org/10.1186/s13059-016-1116-8
• Butler https://github.com/llevar/butler
• adage / yadage https://github.com/diana-hep/adage https://github.com/diana-hep/yadage
• HI-WAY: Execution of Scientific Workflows on Hadoop YARN https://github.com/marcbux/Hi-WAY https://openproceedings.org/2017/conf/edbt/paper-248.pdf
• OpenMOLE https://github.com/openmole/openmole https://www.openmole.org/ https://doi.org/10.3389/fninf.2017.00021
• Biopet https://github.com/biopet/biopet
• Nephele https://nephele.niaid.nih.gov/
• TOPPAS https://doi.org/10.1021/pr300187f
• SBpipe https://pdp10.github.io/sbpipe/ https://github.com/pdp10/sbpipe https://doi.org/10.1186/s12918-017-0423-3
• Dray http://dray.it/
• GenomeVIP https://github.com/ding-lab/GenomeVIP https://doi.org/10.1101/gr.211656.116
• GridSAM https://sourceforge.net/projects/gridsam/
• Roddy https://github.com/eilslabs/Roddy
• SciFlo (historical; doesn't seem to be maintained anymore) https://web.archive.org/web/20161118011409/https://sciflo.jpl.nasa.gov/SciFloWiki/FrontPage
• GNU Guix Workflow Language https://git.roelj.com/guix/gwl.git#gnu-guix-workflow-language-extension https://github.com/UMCUGenetics/guix-workflows/blob/master/umcu/workflows/rnaseq.scm
• Porcupine https://timvanmourik.github.io/Porcupine/
• ECFLOW (Workflow primarily for Meteorological Applications) https://software.ecmwf.int/wiki/display/ECFLOW/ecflow home
• Ophidia http://ophidia.cmcc.it/
• WebLicht https://weblicht.sfs.uni-tuebingen.de/
• GATE Cloud https://cloud.gate.ac.uk/
• SCIPION http://scipion.cnb.csic.es/m/home/ https://github.com/I2PC/scipion/wiki/Creating-a-Protocol
• Ergatis http://ergatis.sourceforge.net/
• TIGR "Workflow" https://sourceforge.net/projects/tigr-workflow/ http://tigr-workflow.sourceforge.net/
• Archivematica https://wiki.archivematica.org/Main_Page (A preservation workflow system that implements the [[ISO-OAIS|https://en.wikipedia.org/wiki/Open_Archival_Information_System]] standard using gearman/MCP)
• Martian http://martian-lang.org/about/
• BioMAJ http://genouest.github.io/biomaj/
• Conveyor http://conveyor.cebitec.uni-bielefeld.de (retired). https://academic.oup.com/bioinformatics/article/27/7/903/230562/Conveyor-a-workflow-engine-for-bioinformatic
• Biopipe http://www.biopipe.org (appears to be defunct) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403782/
• Wildfire http://wildfire.bii.a-star.edu.sg/ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-69
• BioWBI http://bioinformatics.hsanmartino.it/bits_library/library/00079.pdf
• BioWMS http://bioinformatics.hsanmartino.it/bits_library/library/00568.pdf
• BioMoby http://biomoby.open-bio.org/ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-523
• SIBIOS http://ieeexplore.ieee.org/document/1309094/
• NGSANE https://github.com/BauerLab/ngsane https://academic.oup.com/bioinformatics/article/30/10/1471/266879/NGSANE-a-lightweight-production-informatics
• Pwrake https://github.com/misshie/Workflows https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180464/
• Nesoni https://github.com/Victorian-Bioinformatics-Consortium/nesoni
• Skam http://skam.sourceforge.net/skam-intro.html
• TREVA http://bioinformatics.petermac.org/treva/ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095217
• EGene https://www.semanticscholar.org/paper/EGene-a-configurable-pipeline-generation-system-fo-Durham-Kashiwabara/4c0656195b5efcdd3aa7bdcb55fc95a957c150aa https://academic.oup.com/bioinformatics/article/30/18/2659/2475637/EuGene-PP-a-next-generation-automated-annotation
• WEP https://bioinformatics.cineca.it/wep/ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S7-S11
• Microbase http://www.microbasecloud.com/
• e-Science Central http://www.esciencecentral.co.uk/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538293/
• Cyrille2 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-96
• PaPy https://code.google.com/archive/p/papy/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051902/
• JobCenter https://github.com/yeastrc/jobcenter https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-7-8
• CoreFlow https://www.ncbi.nlm.nih.gov/pubmed/24503186
• dynamic-pipeline https://code.google.com/archive/p/dynamic-pipeline/
• XiP http://xip.hgc.jp/wiki/en/Main_Page https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530915/
• Eoulsan http://www.outils.genomique.biologie.ens.fr/eoulsan/ https://www.ncbi.nlm.nih.gov/pubmed/22492314
• CloudDOE http://clouddoe.iis.sinica.edu.tw/
• BioPig https://github.com/JGI-Bioinformatics/biopig https://www.ncbi.nlm.nih.gov/pubmed/24021384
• SeqPig https://github.com/HadoopGenomics/SeqPig https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866557/
• zymake http://www-personal.umich.edu/~ebreck/code/zymake/
• JMS https://github.com/RUBi-ZA/JMS http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134273
• CLC Genomics Workbench https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/
• NG6 http://ng6.toulouse.inra.fr/ https://www.ncbi.nlm.nih.gov/pubmed/22958229
• VIBE http://www.incogen.com/vibe/
• WDL (Workflow Description Language) https://github.com/broadinstitute/wdl
• SciFlow https://github.com/kaizhang/SciFlow (not to be confused with SciFloware and SciFlo).
• Bioshake https://github.com/PapenfussLab/bioshake
• SciPipe http://scipipe.org
• Kapacitor / TICKscripts https://docs.influxdata.com/kapacitor/v1.3//tick/
• AiiDA: Automated Interactive Infrastructure and Database for Computational Science http://www.aiida.net/ https://doi.org/10.1016/j.commatsci.2015.09.013
• Reflow: a language and runtime for distributed, integrated data processing in the cloud https://github.com/grailbio/reflow
• Resolwe: an open source dataflow package for Django framework https://github.com/genialis/resolwe
• Yahoo! Pipes (historical) https://en.wikipedia.org/wiki/Yahoo!_Pipes
• Walrus https://github.com/fjukstad/walrus
• Apache Beam https://beam.apache.org/
• CLOSHA https://closha.kobic.re.kr/ https://www.bioexpress.re.kr/go_tutorial http://docplayer.net/19700397-Closha-manual-ver1-1-kobic-korean-bioinformation-center-kogun82-kribb-re-kr-2016-05-08-bioinformatics-workflow-management-system-in-bio-express.html https://doi.org/10.1186/s12859-018-2019-3
• WopMars https://github.com/aitgon/wopmars http://wopmars.readthedocs.io/
• flowing-clj https://github.com/stain/flowing-clj
• Plumbing and Graph https://github.com/plumatic/plumbing
• LabView http://www.ni.com/en-us/shop/labview.html
• MyOpenLab http://myopenlab.org/
• Max/MSP https://cycling74.com/products/max/
• NoFlo https://noflojs.org/
• Flowstone http://www.dsprobotics.com/flowstone.html
• HyperLoom https://code.it4i.cz/ADAS/loom https://code.it4i.cz/ADAS/loom
• Dask http://dask.pydata.org/en/latest/ https://github.com/dask/dask
• Stimela https://github.com/SpheMakh/Stimela https://github.com/SpheMakh/Stimela/wiki https://www.acru.ukzn.ac.za/~cosmosafari2017/wp-content/uploads/2017/02/makhathini.pdf
• JTracker https://jtracker.io/ https://github.com/jtracker-io
• PipelineDog http://pipeline.dog/ https://github.com/zhouanbo/pipelinedog https://doi.org/10.1093/bioinformatics/btx759
• DALiuGE https://arxiv.org/abs/1702.07617 https://github.com/ICRAR/daliuge https://daliuge.readthedocs.io/
• Overseer https://github.com/framed-data/overseer
• Squonk https://squonk.it/
• GC3Pie https://github.com/uzh/gc3pie
• Fractalide https://github.com/fractalide/fractalide
• TOGGLe http://toggle.southgreen.fr/ https://doi.org/10.1101/245480
• Askalon http://www.askalon.org
• Eclipse ICE (The Integrated Computational Environment) https://www.eclipse.org/ice
• Sandia Analysis Workbench (SAW) http://www.sandia.gov/saw/
• dispel4py https://github.com/dispel4py/dispel4py
• Jobber https://pypi.python.org/pypi/Jobber/0.1.4
• NeatSeq-Flow http://neatseq-flow.readthedocs.io/
• S4M https://bitbucket.org/uqokorn/s4m_base/wiki/Home
• Loom http://med.stanford.edu/gbsc/loom.html https://github.com/StanfordBioinformatics/loom http://loom.readthedocs.io/en/latest/templates.html
• Watchdog - XML Schema-based bioinformatics workflow system https://www.bio.ifi.lmu.de/software/watchdog/ https://doi.org/10.1186/s12859-018-2107-4 https://github.com/klugem/watchdog
• phpflo https://github.com/phpflo/phpflo
• BASTet: Berkeley Analysis and Storage Toolkit https://openmsi.nersc.gov/openmsi/client/bastet.html https://biorack.github.io/BASTet/ https://doi.org/10.1109/TVCG.2017.2744479
• Tavaxy: Pattern based workflow system for the bioinformatics domain http://www.tavaxy.org/
• Ginflow: Decentralised adaptive workflow engine https://ginflow.inria.fr/
• SciApps: A cloud-based platform for reproducible bioinformatics workflows https://doi.org/10.1093/bioinformatics/bty439 https://www.sciapps.org/
• Stoa: Script Tracking for Observational Astronomy https://github.com/petehague/Stoa
• Collective Knowledge (CK) framework http://cknowledge.org/
• QosCosGrid (QCG) http://www.qoscosgrid.org/ http://www.qoscosgrid.org/trac/qcg-broker/wiki/qcg-advanced-client
• High-Throughput Binding Affinity Calculator (HTBAC) https://htbac.readthedocs.io/en/latest/ https://github.com/radical-cybertools/htbac https://arxiv.org/abs/1801.01174
• BioWorkbench (Swift-based) https://arxiv.org/abs/1801.03915 https://github.com/mmondelli/bioworkbench
• ENVI Task Engine https://gbdxdocs.digitalglobe.com/docs/envi-task-engine https://www.harrisgeospatial.com/Learn/Whitepapers/TabId/2359/ArtMID/10212/ArticleID/17299/Workflow-Tools-in-ENVI.aspx https://envi-py-engine.readthedocs.io/en/latest/index.html
• Pypeline https://github.com/cgarciae/pypeln
• mpipe http://vmlaker.github.io/mpipe/
• idseq-dag https://github.com/chanzuckerberg/idseq-dag
• Piper (based upon GATK Queue) https://github.com/NationalGenomicsInfrastructure/piper
• Apache Object Oriented Data Technology (OODT) http://oodt.apache.org/
• JX Workflow (DSL for Makeflow) https://ccl.cse.nd.edu/software/manuals/jx-quick.html http://ccl.cse.nd.edu/research/papers/jx-escience-2018.pdf
• The Adaptable IO System (ADIOS), ADIOS using applications can be the orchestrated into a workflow http://csmd.ornl.gov/adios
• GenPipes https://bitbucket.org/mugqic/genpipes https://doi.org/10.1101/459552
• Argo https://argoproj.github.io/ https://github.com/argoproj/argo https://github.com/argoproj/argo/blob/master/examples/README.md
• Reana https://reana.readthedocs.io/en/latest/ https://github.com/reanahub/reana
• Cuisine Framework https://www.astron.nl/~renting/cuisine.html
• Niassa https://github.com/oicr-gsi/niassa https://oicr-gsi.github.io/niassa-docs/
• pypeFLOW https://github.com/PacificBiosciences/pypeFLOW
• Tiny Cloud Engine http://ka.cb.k.u-tokyo.ac.jp/tce/
• Xbowflow https://github.com/ChrisSuess/Project-Xbow/tree/master/xbowflow
• AdaptiveMd https://github.com/markovmodel/adaptivemd
• Meshroom https://github.com/alicevision/meshroom
• LSST Data Management https://github.com/lsst/pipe_base
• CGAT-core https://github.com/cgat-developers/cgat-core
• Prefect https://docs.prefect.io/
• Apache SCXML engine https://commons.apache.org/proper/commons-scxml/guide/core-engine.html https://commons.apache.org/proper/commons-scxml/guide/scxml-documents.html
• IceProd https://github.com/WIPACrepo/iceprod
• AnADAMA2 http://huttenhower.sph.harvard.edu/anadama2
• Luna https://luna-lang.org/
• Passerelle https://code.google.com/archive/a/eclipselabs.org/p/passerelle
• Kurator-Akka https://github.com/kurator-org/kurator-akka
• Jug https://doi.org/10.5334/jors.161
• Node-RED https://nodered.org/
• Databolt Flow https://github.com/d6t/d6tflow
• Frictionless Data Package Pipelines https://github.com/frictionlessdata/datapackage-pipelines
• DataFlows https://github.com/datahq/dataflows
• Volcano https://github.com/volcano-sh/volcano
• DataJoint https://datajoint.io/
• DIRAC3 (LHCb grid software) https://doi.org/10.1088/1742-6596/219/6/062029
• Orange https://orange.biolab.si/ http://jmlr.org/papers/v14/demsar13a.html
• Ensemble Toolkit (EnTK) https://radicalentk.readthedocs.io/en/latest/entk.html https://arxiv.org/abs/1602.00678v2
• BioQueue http://www.bioqueue.org/ https://github.com/liyao001/BioQueue https://doi.org/10.1093/bioinformatics/btx403
• mlr3pipelines https://mlr3pipelines.mlr-org.com/
• Kedro - Production-Ready Data & ML Pipelines https://github.com/quantumblacklabs/kedro
• DATAVIEW - DATAVIEW is a big data workflow management system. https://github.com/shiyonglu/DATAVIEW
• SecDATAVIEW - SecDATAVIEW is a security oriented big data workflow management system compatible with the heterogeneous computing environments. https://github.com/shiyonglu/SecDATAVIEW
• Giraffe Tools https://giraffe.tools/
• CERAMICCA - Cloud Engine Resource for Accelerated Medical Image Computing for Clinical Applications: https://ceramicca.ensc.sfu.ca
• uap - Universal Analysis Pipeline. A workflow management system dedicated to robust, consistent, and reproducible HTS data analysis. https://github.com/yigbt/uap
• signac https://signac.io/
• cwltool - reference implementation of Common Workflow Language (CWL) https://github.com/common-workflow-language/cwltool/
• CWLEXEC - CWL executor for IBM Spectrum LSF clusters https://github.com/IBMSpectrumComputing/cwlexec
• drmr https://github.com/ParkerLab/drmr/ https://drmr.readthedocs.io/
• Autosubmit - a versatile tool to manage Weather and Climate Experiments in diverse Supercomputing Environments. https://www.bsc.es/research-and-development/software-and-apps/software-list/autosubmit https://autosubmit.readthedocs.io/en/latest/
• JUDI https://doi.org/10.1093/bioinformatics/btz956 https://github.com/ncbi/JUDI
• Sumatra - a tool for managing and tracking projects based on numerical simulation or analysis, with the aim of supporting reproducible research https://neuralensemble.org/sumatra/
• Netflix Conductor: https://netflix.github.io/conductor/
• Pipengine https://doi.org/10.21105/joss.00341 https://github.com/fstrozzi/bioruby-pipengine
• MyQueue https://doi.org/10.21105/joss.01844 https://gitlab.com/myqueue/myqueue
• Drake R package https://doi.org/10.21105/joss.00550 https://github.com/ropensci/drake
• MaDaTS https://10.21105/joss.00830 https://github.com/dghoshal-lbl/madats