Bioinformatics-Workflow-Frameworks.v6.3.8 @albertvilella
 Share
The version of the browser you are using is no longer supported. Please upgrade to a supported browser.Dismiss

View only
 
ABCDEFGHILMNOPQRS
1
#Bioinformatics #WorkflowManagers #Tools #Platform #Languages #Specifications #StandardsSubscribers score github = watch+(star/5)+(fork*10)Poll votes https://bit.ly/biowlpRepo Score 02Repo Score 03Repo Score 04Repo Score 05Repo Score 06Repository URLRepo watchedGithub starredRepo forkedcommitsbranchesreleasescontributorslanguages
2
GalaxyProject @galaxyproject5508.6141178711.65975625756.6https://github.com/galaxyproject/galaxy6258353313153209Python;XML;JavaScript;reStructuredText;Mako;Shell;Text;YAML;CSS;Vue
3
nipype415908815414499544375https://github.com/nipy/nipype54425402121521Python;reStructuredText;Tcl;Shell;Text;HTML;Markdown;YAML;INI;JSON
4
bcbio @chapmanb3188.851064524.83728943564.8https://github.com/bcbio/bcbio-nextgen9467429614511Python;YAML;Shell;reStructuredText;JSON;Text;SVG;CSV;Lua;Markdown
5
NextFlow @NextFlowIO2000.41301032398.42634622248.4https://github.com/nextflow-io/nextflow627921781251591Groovy;Nextflow;Java;reStructuredText;Shell;Text;HTML;Gradle;Markdown;JavaScript
6
SnakeMake @johanneskoester1851.6186433294.61990872199.6https://bitbucket.org/Snakemake/Snakemake/87173173
7
toil @TerraBioApp1809.80814342.82281622057.8https://github.com/DataBiosphere/toil62589163
8
Cromwell @broadinstitute1435.80629301.81763941811.8https://github.com/broadinstitute/cromwell944091261168471Scala;wdl;Common_Workflow_Language;JSON;XML;Markdown;Text;Shell;Java;YAML
9
Fireworks1147.40328202.41273661411.4https://github.com/materialsproject/fireworks661571051101831reStructuredText;Python;HTML;YAML;JavaScript;Text;Less;SCSS;CSS;Shell
10
HTCondor @HTCondor813.41243129.492725913.4https://github.com/htcondor/htcondor251427612843631C;Perl;Batchfile;C;TeX;reStructuredText;CMake;Python;Shell;Diff
11
Arvados @VeritasGenetics765.62315144.693633897.6https://github.com/curoverse/arvados3321369116111Ruby;Go;Python;HTML;Liquid;R;Shell;Common_Workflow_Language;Java;JavaScript
12
CloudSlang764.20296143.291736908.2https://github.com/CloudSlang/cloud-slang36191691262171Slash;Java;YAML;XML;INI;Maven_POM;Markdown;Text;CSS;JavaScript
13
DNAnexus @dnanexus635.69178131.668264891.6https://github.com/dnanexus/dx-toolkit64585611305411R;Python;C;Java;Shell;Markdown;JSON;Makefile;reStructuredText;Text
14
Luigi/Sciluigi561.65323120.676421645.6https://github.com/pharmbio/sciluigi2125349296171Python;Text;Shell;Markdown;reStructuredText
15
BPipe468.6220990.658719544.6https://github.com/ssadedin/bpipe1914842125151Shell;Groovy;Text;Markdown;Java;CSV;HTML;Gradle;YAML;Roff
16
Scipipe555.43608186.497740715.4https://github.com/scipipe/scipipe40527418629201Go;Markdown;Shell;YAML;SVG;CSS;Text
17
Knime561.40249111.469927669.4https://github.com/knime/knime-core271725011841011XML;Java;SVG;HTML;INI;Text;Unity3D_Asset;Ant_Build_System;JSON;Maven_POM
18
reflow @grailbio436.20624175.288534572.2https://github.com/grailbio/reflow3456129440191Go;Markdown;Text;Yacc;CSV;JSON;SVG;YAML
19
Pipeliner350.606453.636118422.6https://github.com/CCBR/Pipeliner18133314121Ragel;Python;R;Perl;Roff;JSON;Shell;RMarkdown;JavaScript;CSS
20
Cosmos337.2010358.238216401.2https://github.com/LPM-HMS/COSMOS2165631143801Python;reStructuredText;HTML;CSS;SVG;JavaScript;Less;INI;Makefile;Markdown
21
Ruffus @CGAT_Oxford317.8017365.842511361.8https://github.com/cgat-developers/ruffus11134281461reStructuredText;Python;Graphviz_;SVG;HTML;Text;Batchfile;Makefile;Assembly;CSS
22
Unipro UGENE269.4012062.432725369.4https://github.com/ugeneunipro/ugene257223165271C;C;XML;QMake;Text;CMake;Python;Shell;Batchfile;JavaScript
23
BigDataScript25601134932010296https://github.com/pcingola/BigDataScript108023123381Java;Text;Shell;Perl;CSV;Go;XML;HTML;Assembly;INI
24
pyflow @illumina275.4413868.434528387.4https://github.com/illumina/pyflow2887231183231Python;Shell;Text;Markdown;C;YAML;INI
25
OpenMOLE27601406035616340https://github.com/openmole/openmole1610024133591Scala;SVG;Java;HTML;Shell;TeX;CSS;JSON;INI;Markdown
26
Wings252.47545.428215312.4https://github.com/KnowledgeCaptureAndDiscovery/wings153723382511Java;Web_Ontology_Language;JavaScript;HTML;Maven_POM;Java_Server_Pages;XML;INI;CSS;YAML
27
Seven Bridges Genomics2300875925833362https://github.com/sbg/sevenbridges-python3335193173601Python;reStructuredText;Markdown;INI;Text;YAML;Batchfile;Makefile
28
@gnutools make274.607140.63057302.6https://github.com/mirror/make7382613641Perl;C;Makefile;DIGITAL_Command_Language;Roff;Shell;Text;Batchfile;M4Sugar;C
29
NGSANE2320714326015292https://github.com/BauerLab/ngsane15352114181Shell;Text;Python;R;TeX;JavaScript;CSS;HTML;Makefile;Perl
30
AWE242.28944.228711286.2https://github.com/MG-RAST/AWE11562214471Go;Markdown;Shell;Text;Dockerfile;Protocol_Buffer;Unix_Assembly;C;YAML;HTML
31
eHive / ensembl-hive @ensembl2560774928419332https://github.com/Ensembl/ensembl-hive193523123861Perl;SQL;Graphviz_;reStructuredText;PLpgSQL;Python;Shell;Java;Markdown;Text
32
Cluster Flow225.810545.828511269.8https://github.com/ewels/ClusterFlow117420852261Perl;Markdown;HTML;Python;Text;R;YAML
33
WES @ga4gh198.808254.822632326.8https://github.com/ga4gh/workflow-execution-service-schemas323416212641Python;Text;Markdown;Shell;AsciiDoc;Gradle;JSON;JavaScript;YAML;HTML
34
pypeFLOW @PacBio @illumina197.803426.82056221.8https://github.com/PacificBiosciences/pypeFLOW6919493781Python;reStructuredText;JSON;Shell;Makefile;Markdown;Text;YAML
35
Cpipe146.85329.817011190.8https://github.com/MelbourneGenomics/cpipe11291335616201C;C;Shell;Makefile;Text;reStructuredText;Python;Perl;HTML;SQL
36
Cuneiform14681514725010186https://github.com/joergen7/cuneiform10130115362111Erlang;Markdown;Shell;Text;YAML;Ignore_List
37
Makeflow149.65132.616815209.6https://github.com/cooperative-computing-lab/makeflow-examples152313140101Perl;Markdown;Python;JSON;Shell;C;Ignore_List
38
JMS116.602817.61274132.6https://github.com/RUBi-ZA/JMS41311109401JavaScript;HTML;CSS;Less;Python;SCSS;JSON;Markdown;Text;SVG
39
DiscoveryEnvironment117.63427.612416181.6https://github.com/cyverse-archive/DiscoveryEnvironmentBackend1681016171Clojure;SQL;Go;Markdown;XML;Shell;EBNF;Text;Dockerfile;JSON
40
JobCenter103021131111107https://github.com/yeastrc/jobcenter110101062171Java;XML;Text;INI;CSS;Java_Server_Pages;Ant_Build_System;JavaScript;SQL;Shell
41
Flowr101081291538133https://github.com/sahilseth/flowr86587645111R;Shell;RMarkdown;Markdown;YAML;Text;JavaScript
42
Ketrew110943816616174https://github.com/hammerlab/ketrew16708115121OCaml;Markdown;Shell;CSS;Dockerfile;JSON;Makefile;SVG;Text;YAML
43
Pegasus110943816616174https://github.com/hammerlab/ketrew16708115121OCaml;Markdown;Shell;CSS;Dockerfile;JSON;Makefile;SVG;Text;YAML
44
BioPig96.604942.610335236.6https://github.com/JGI-Bioinformatics/biopig3586305121Java;PigLatin;Text;XML;INI;Maven_POM;Shell
45
FireCloud @BroadFireCloud / WDL84.405448.49043256.4https://github.com/broadinstitute/firecloud-tools4374681201Python;Markdown;Shell;wdl;Dockerfile;Text
46
Loom99.804727.811915159.8https://github.com/StanfordBioinformatics/loom1524817721Python;YAML;JavaScript;HTML;Text;Shell;CSS;reStructuredText;SVG;Ruby
47
SeqPig88.802416.8967116.8https://github.com/HadoopGenomics/SeqPig798287151Java;PigLatin;Shell;Perl;TeX;Text;Makefile;Maven_POM;Python;R
48
TOGGle79.644025.69416143.6https://github.com/SouthGreenPlatform/TOGGLE161865692101Perl;Text;TeX;Markdown;Shell
49
Triquetrum7327198111117https://github.com/eclipse/triquetrum111065541781Java;XML;INI;HTML;Maven_POM;Python;Markdown;CSS;Text
50
Stacks101.24120.21226125.2https://github.com/enormandeau/stacks_workflow62696761101Shell;Python;R;CSV;Markdown;Text;Ignore_List
51
BioMake66.816921.8114586.8https://github.com/evoldoers/biomake55954121281Makefile;Prolog;Text;Perl;Markdown;Shell;NewLisp;SQL;YAML;Regular_Expression
52
Copernicus59.82214.867891.8https://github.com/gromacs/copernicus895619951Python;Shell;XML;reStructuredText;Text;INI;Makefile;Batchfile;C;CSS
53
Noodles58.62413.669682.6https://github.com/NLeSC/noodles6135553681Python;SVG;Jupyter_Notebook;C;reStructuredText;INI;JSON;Markdown;Text;YAML
54
Mistral63.8139.867375.8https://github.com/arteria-project/arteria-core34659181Python;INI;Text;Markdown;YAML
55
Stimela66029217414122https://github.com/SpheMakh/Stimela14105113251Dockerfile;Python;Shell;JSON;Makefile;Markdown;HTML;INI;Text;YAML
56
GenomeVIP44.802917.8561292.8https://github.com/ding-lab/GenomeVIP12143104191PHP;Perl;reStructuredText;CSS;HTML;JavaScript;Shell;Batchfile;Text;ApacheConf
57
BioDSL35.6198.646347.6https://github.com/maasha/BioDSL313313341Ruby;Haml;Markdown;Text
58
DNAstack @DNAstack3407734450https://github.com/DNAstack/ga4gh-discovery-service-registry-impl40359501
59
Agave32.265.233240.2https://github.com/agaveapi/docker-runner-webapp-demo2136201JavaScript;CSS;HTML;XML;CoffeeScript;SVG;Less;JSON;Markdown;Text
60
Chipster29.81511.833965.8https://github.com/chipster/chipster-tools942121401HTML;R;Python;Shell;Text;JSON;JavaScript;XML;Gradle;Batchfile
61
Yabi27.8179.835651.8https://github.com/muccg/yabi692131541JavaScript;CSS;Python;JSON;PLpgSQL;HTML;reStructuredText;SVG;Shell;YAML
62
Kronos26.2218.239338.2https://github.com/jtaghiyar/kronos316259241Python;Markdown;Text
63
CGAT-core69.202815.282693.2https://github.com/cgat-developers/cgat-core61662794141Python;reStructuredText;Text;Shell;YAML;Makefile;Markdown
64
BioSAILs13.8124.821221.8https://github.com/biosails/pheniqs291416371C;JSON;Python;Markdown;Shell;R;XML;CSV;YAML;C
65
pypipegraph22.674.625230.6https://github.com/TyberiusPrime/pypipegraph2324681101Python;reStructuredText;INI;Text;YAML;Makefile;Markdown;TOML
66
Pwrake23.20145.232127.2https://github.com/misshie/Workflows111221101Ruby;RDoc;Markdown;Shell
67
YesWorkflow21.453.423125.4https://github.com/yesworkflow-org/yw122411161C;XML;Makefile;C;PowerShell;ANTLR;Graphviz_;Markdown;Python;SVG
68
Niassa @OICR_news / Apache Oozie12.831612.8161260.8https://github.com/oicr-gsi/niassa12401531Java;SQL;JSON;XML;Java_Properties;INI;Shell;Maven_POM;Text;Markdown
69
Chronos18.2109.219850.2https://github.com/phnmnl/workflow-demo811190701Markdown;Dockerfile;Shell;JSON;R;CSS;JavaScript;PHP;Jupyter_Notebook;Text
70
@lifebitAI local-deploit3333315https://github.com/lifebit-ai/local-deploit3000000
71
SBpipe134413325https://github.com/pdp10/sbpipe3011351Python;YAML;Component_Pascal;CSV;reStructuredText;R;Text;Markdown;Shell;INI
72
COMBUSTI/O12.8073.816220.8https://github.com/jarlebass/combustio2411101Scala;XML;Java;Shell;INI;CSS;Markdown;Text;XSLT
73
BioCloud12.4053.414220.4https://github.com/ccwang002/biocloud-server-kai221258101SCSS;Python;HTML;JavaScript;Text;CSS;Markdown;INI;SVG
74
Dog12.243.213220.2https://github.com/zhouanbo/pipelinedog211122261
JavaScript;JSON;JSX;Text;Shell;CSS;HTML;Markdown;SVG
75
JUDI131313131365https://github.com/ncbi/JUDI130039101reStructuredText;Python;Text;Batchfile;Makefile;Markdown;Shell
76
qsubsec12.493.418116.4https://github.com/alastair-droop/qsubsec17176131Python;Markdown;Text
77
None / Own scripts0240000
78
Apache Taverna020000
79
GenePattern00000http://software.broadinstitute.org/cancer/software/genepattern
80
Anvaya00000http://www.ncbi.nlm.nih.gov/pubmed/22809419
81
WopMars112211115https://github.com/aitgon/wopmars101406261Python;YAML;reStructuredText;Text;INI;Makefile
82
BioDT00000
83
Bioboxes68181472796https://github.com/bioboxes/command-line-interface756397551Python;Shell;Gherkin;Markdown;Text;YAML;Dockerfile;INI;Makefile
84
WDL @WDL_Dev960.47119105.49747988.4https://github.com/broadinstitute/wdl717953841641
85
Airavata1014.4187141.41060331146.4https://github.com/apache/airavata335797125171Java;C;YAML;Python;PHP;Maven_POM;Thrift;Shell;XML;SQL
86
CWL-Airflow://github.com/Barski-lab/cwl-airflow
87
Orcahttps://github.com/bcgsc/orca10217340171Dockerfile;Markdown;YAML;Shell;R;Makefile;Text
88
Biocontainers1256NA4392031492271364https://github.com/BioContainers/containers272951171111Dockerfile;Text;Shell;Perl;Markdown;Python;Makefile;Perl_6;R
89
Pinball1542.41163381.42324571770.4https://github.com/pinterest/pinball57977129150701Python;JavaScript;CSS;HTML;reStructuredText;SVG;Text;YAML;Shell;INI
90
Leaf288646946528901953666https://github.com/autumnai/leaf1955269164461Rust;Markdown;HTML;CSS;TOML;JavaScript;Cap;SVG;Shell;YAML
91
Singularity2851.2NA377376.228521013255.2https://github.com/sylabs/singularity10112751155294Go;Markdown;Text;JSON;Shell;YAML;Unix_Assembly;Makefile;C;Alpine_Abuild
92
Bioconda305.2NA1049296.21058107733.2https://github.com/bioconda/bioconda-recipes1079411126821Shell;YAML;Diff;Python;Text;Perl;Markdown;SVG;C;Roff
93
Azkaban256.4249247.42582461240.4https://github.com/azkaban/azkaban246211111171Java;JavaScript;INI;SQL;Gradle;Shell;Less;CSS;reStructuredText;HTML
94
Docker containers213.8NA208204.82172031025.8https://github.com/docker/docker-py2034111496310Python;reStructuredText;INI;Markdown;Text;Dockerfile;Shell;YAML;CSS;Groovy
95
Apache Beam @ApacheBeam241.40234232.42432311165.4https://github.com/apache/beam23121132109433Java;Python;Go;Markdown;Gradle;Groovy;SCSS;Shell;YAML;HTML
96
Airflow685.4659649.46956433257.4https://github.com/apache/airflow64312418111794Python;reStructuredText;HTML;Text;Shell;YAML;Markdown;INI;XML;JavaScript
97
Apache NiFi0000
98
QuickNGS0000
99
GATK Queue @broadinstitute0000
100
sushi0000
Loading...