Modular and universal bioinformatics
Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.
Project Board
Backlog 62
Image at the bottom of readme file is broken.
bionode/bionode-sam#5 opened by yeban
documentationmozsprint
Add a .travis.yml file with Node environment
bionode/events#2 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-scripts#2 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-blast#2 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/gsoc16#16 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/try-bionode#4 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-obo#26 opened by bmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-quickgo#2 opened by bmpvieira
mozsprinttest
Add MIT LICENSE file and change it from ISC in package.json
bionode/github-project-public#3 opened by bmpvieira
legalmozsprint
Check if file is empty
bionode/bionode-watermill#51 opened by tiagofilipe12
bugmozsprint
Pipeline Graph (DAG) Visualization
bionode/bionode-watermill#50 opened by thejmazz
featuremozsprint
Convert from wrapper to native module
bionode/bionode-sam#3 opened by bmpvieira
featuremozsprint
consider renaming this module
bionode/fasta-parser#3 opened by tiagofilipe12
discussion
Integrate nodestream
bionode/bionode-watermill#46 opened by thejmazz
discussionmozsprint
bionode-seq features as Atom.io plugin
bionode/bionode-seq#4 opened by ilevantis
featuremozsprint
Common Workflow Language (CWL) support?
bionode/bionode-watermill#45 opened by olgabot
CWLdiscussionmozsprint
flag to allow input resolution to fallback to cwd
bionode/bionode-watermill#44 opened by thejmazz
enhancement
better logs when input is not resolved
bionode/bionode-watermill#43 opened by thejmazz
enhancement
Custom file validator over output object
bionode/bionode-watermill#42 opened by thejmazz
feature
json schema validator on input, output, action stream
bionode/bionode-watermill#39 opened by thejmazz
enhancementvalidators
Trinity Pipeline
bionode/bionode-watermill#37 opened by thejmazz
examples
Parallelize BAM chunks
bionode/bionode-watermill#36 opened by thejmazz
examples
Basic CLI
bionode/bionode-watermill#31 opened by thejmazz
feature
Example Pipelines
bionode/bionode-watermill#30 opened by thejmazz
enhancementepic
Advanced genomic vcf workflow
bionode/bionode-watermill#29 opened by thejmazz
enhancement
Reentrancy
bionode/bionode-watermill#27 opened by thejmazz
epicfeature
tee stream to file
bionode/bionode-watermill#26 opened by thejmazz
feature
File Validation
bionode/bionode-watermill#22 opened by thejmazz
epicfeature
Unit tests for task orchestration
bionode/bionode-watermill#18 opened by thejmazz
enhancementepic
complex join, parallels, forking
bionode/bionode-watermill#16 opened by thejmazz
test
transform task
bionode/bionode-watermill#15 opened by thejmazz
test
simple forking
bionode/bionode-watermill#14 opened by thejmazz
test
Parallelization?
bionode/bionode-sra#4 opened by olgabot
question
ES6 Discussion
bionode/bionode#33 opened by thejmazz
discussion
Remove zlib dependency, replace with core Node api
bionode/bionode-fasta#6 opened by thejmazz
enhancement
Integrate with OBO 1.2 spec
bionode/bionode-obo#7 opened by thejmazz
enhancement
Identify all stanza, tag types
bionode/bionode-obo#6 opened by thejmazz
enhancement
Stanza parser
bionode/bionode-obo#20 opened by thejmazz
test
Handle unrecognized tags
bionode/bionode-obo#16 opened by thejmazz
enhancement
Handle trailing modifiers
bionode/bionode-obo#9 opened by thejmazz
enhancement
Handle escape characters
bionode/bionode-obo#10 opened by thejmazz
enhancement
Handle dangling references
bionode/bionode-obo#17 opened by thejmazz
enhancement
Handle comments
bionode/bionode-obo#8 opened by thejmazz
enhancement
Define/follow serializer conventions
bionode/bionode-obo#18 opened by thejmazz
enhancement
Define spec requirements with json
bionode/bionode-obo#15 opened by thejmazz
enhancement
Check for id, name, instance_of in [Instance]
bionode/bionode-obo#14 opened by thejmazz
enhancement
Check for id, name in [Term] stanza
bionode/bionode-obo#12 opened by thejmazz
enhancement
Enhancement: more lessons!
bionode/biohacker#1 opened by 100ideas
enhancementmozsprint
RequireBin FLAGRANT SYSTEM ERROR
bionode/bionode#31 opened by shotlom
bug
Make Docker image and users /home more lightweight
bionode/try-bionode#1 opened by bmpvieira
enhancement
Write wrapper around qsub
bionode/bionode-sge#2 opened by bmpvieira
featurehelp wanted
Issues with modules that require binaries (wrappers)
bionode/bionode#29 opened by bmpvieira
discussionhelp wanted
Autogenerate module template
bionode/bionode#23 opened by bmpvieira
enhancementmozsprint
sam parser in bionode
bionode/bionode#17 opened by wilzbach
enhancementhelp wanted
Refactor to be more like other bionode modules
bionode/bionode-bbi#1 opened by bmpvieira
enhancementhelp wanted
Add documentation, and more info to README.md
bionode/bionode-bbi#2 opened by bmpvieira
documentationhelp wanted
Add tests
bionode/bionode-sam#1 opened by bmpvieira
enhancement
Add documentation
bionode/bionode-sam#2 opened by bmpvieira
enhancement
Next 6
CLI implementation
bionode/bionode-fastq#8 opened by tiagofilipe12
enhancementmozsprint
User-friendly CLI
bionode/bionode#25 opened by c089
enhancement
Better handling of STDERR and STDOUT
bionode/bionode#41 opened by bmpvieira
enhancement
Add command line interface (CLI)
bionode/bionode-seq#5 opened by bmpvieira
feature
Improve global documentation generation and layout
bionode/bionode#27 opened by bmpvieira
enhancement
Modularize lib structure.
bionode/bionode-ncbi#34 opened by Istar-Eldritch
enhancement
In Progress 23
Explain template literals
bionode/bionode-watermill-tutorial#1 opened by tiagofilipe12
enhancement
Output some warning to terminal when there is no output
bionode/bionode-ncbi#38 opened by tiagofilipe12
enhancementux
Added a .travis.yml file.
bionode/bionode-obo#27 opened by StuntsPT
enhancementmozsprint
Added a .travis.yml file.
bionode/bionode-scripts#3 opened by StuntsPT
enhancementmozsprint
Added a .travis.yml file.
bionode/bionode-blast#3 opened by StuntsPT
enhancementmozsprint
Added .travis.yml node.js environment. Fixes #2.
bionode/events#3 opened by StuntsPT
enhancementmozsprint
Added .travis.yml node.js environment. Fixes #2.
bionode/bionode-quickgo#3 opened by StuntsPT
enhancementmozsprint
Added a license file.
bionode/github-project-public#4 opened by StuntsPT
enhancementmozsprint
Standardization
bionode/bionode-sam#6 opened by StuntsPT
enhancementmozsprint
Standardization
bionode/bionode-sra#7 opened by StuntsPT
enhancementmozsprint
Standardization
bionode/bionode-gff#3 opened by StuntsPT
enhancementmozsprint
Standardized README.md
bionode/bionode-fastq#9 opened by StuntsPT
enhancement
Standardization
bionode/bionode-vcf#6 opened by StuntsPT
enhancementmozsprint
Refactoring to use stream modules
bionode/bionode-fastq#7 opened by tiagofilipe12
enhancementmozsprint
Corrected a typo and improved line spacings.
bionode/bionode-ncbi#37 opened by StuntsPT
enhancementmozsprint
Do the db filter at lib level
bionode/bionode-ncbi#33 opened by Istar-Eldritch
featuremozsprint
geo is not searchable
bionode/bionode-ncbi#20 opened by lorenzorietti
enhancementmozsprint
Simple usage tutorial
bionode/bionode-watermill#49 opened by tiagofilipe12
documentationmozsprint
Follow the JavaScript Standard style
bionode/bionode#26 opened by bmpvieira
choremozsprint
Styleguide for tagging
bionode/bionode#39 opened by bmpvieira
choremozsprint
Done 192
only push when not a PR
bionode/bionode.github.io#11 opened by IsmailM
bug
Add obf
bionode/bionode.github.io#9 opened by IsmailM
community
Mozilla's Global Sprint (June 1st and 2nd 2017)
bionode/bionode#44 opened by bmpvieira
communitymozsprint
Roadmap
bionode/bionode#42 opened by bmpvieira
discussionmozsprint
Recognise all kinds of contributions
bionode/bionode#43 opened by bmpvieira
communitymozsprint
How can be a pipeline extended to deal with multiple samples?
bionode/bionode-watermill#47 opened by zhangzhen
mozsprintquestion
Standardization
bionode/bionode#45 opened by StuntsPT
enhancementmozsprint
Code of Conduct
bionode/bionode#38 opened by bmpvieira
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/events#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-bbi#3 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/biohacker#2 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-sam#4 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-examples#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-go#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-seq#6 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/docker-browser-server#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-flow#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-gff#2 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-fastq#6 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-quickgo#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-obo#25 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/try-bionode#3 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/gsoc16#15 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-scripts#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-blast#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-vcf#5 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode.github.io#8 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/github-project-public#2 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/get-bionode#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-sra#6 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-fasta#9 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/doc.bionode.io#3 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-watermill#52 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/GSoC17#1 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-bwa#2 opened by ayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-template#3 opened by ayangromano
communitymozsprint
Standardize
bionode/bionode-template#2 opened by StuntsPT
enhancementmozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-ncbi#36 opened by ayangromano
communitymozsprint
Standardization
bionode/bionode-bwa#1 opened by StuntsPT
enhancementmozsprint
module links in readme are 404
bionode/bionode#30 opened by acthp
communitymozsprint
Standardization
bionode/bionode-ncbi#35 opened by StuntsPT
enhancementmozsprint
Highlight other projects using Bionode tools
bionode/bionode.github.io#6 opened by bmpvieira
community
Add Users and Acknowledgement sections
bionode/bionode.github.io#7 opened by IsmailM
community
correct path to home folder
bionode/bionode-watermill#48 opened by tiagofilipe12
bug
Responsive columns
bionode/github-project-public#1 opened by IsmailM
enhancement
fix typos
bionode/doc.bionode.io#2 opened by IsmailM
documentation
Fix bionode-ncbi example
bionode/doc.bionode.io#1 opened by erictleung
documentation
Old Roadmap
bionode/bionode#35 opened by bmpvieira
discussion
make the font-size larger (1.4rem) in the about section
bionode/bionode.github.io#5 opened by IsmailM
enhancement
Update CONTRIBUTE.md
bionode/bionode#36 opened by bmpvieira
community
Error handling when NCBI connection is lost
bionode/bionode-ncbi#29 opened by tiagofilipe12
discussion
User-friendly CLI
bionode/bionode-ncbi#31 opened by bmpvieira
enhancement
Better CLI, this fixes #31, #29, #20 and #11
bionode/bionode-ncbi#32 opened by bmpvieira
enhancement
add events section to the website
bionode/bionode.github.io#4 opened by IsmailM
community
update website content
bionode/bionode.github.io#3 opened by IsmailM
chore
Update on docs, removing a useless comment
bionode/bionode-ncbi#28 opened by tiagofilipe12
documentation
Git rid of git-lfs
bionode/bionode-ncbi#25 opened by bmpvieira
test
Remove git-lfs
bionode/bionode-ncbi#26 opened by bmpvieira
test
Progress bar
bionode/bionode-ncbi#23 opened by tiagofilipe12
ux
Timeline
bionode/bionode-watermill#2 opened by thejmazz
discussion
v0.2.x
bionode/bionode-watermill#40 opened by thejmazz
discussion
Make project board public
bionode/bionode#40 opened by bmpvieira
community
Upkeep
bionode/fasta-parser#2 opened by Rudani
chore
Raise error on failed parsing and ignore empty stream
bionode/fasta-parser#1 opened by drpowell
enhancement
Fix code to follow StandardJS style guide
bionode/bionode-fasta#8 opened by Rudani
chore
Fix tests (#18) and mocking NCBI API
bionode/bionode-ncbi#21 opened by bmpvieira
bug
Add a Gitter chat badge to README.md
bionode-hack/bionodered#1 opened by gitter-badger
enhancement
Dependency removal (fs)
bionode/bionode-vcf#4 opened by amblina
bug
rna_from_genomic instead of genomic.fna
bionode/bionode-ncbi#19 opened by thejmazz
bug
Papers
bionode/gsoc16#10 opened by thejmazz
discussion
Google Summer of Code 2015
bionode/bionode#28 opened by bmpvieira
community
Update index.js
bionode/bionode-vcf#3 opened by wookoouk
deprecated
Week 1
bionode/gsoc16#9 opened by thejmazz
discussion
VC workflows comparison
bionode/gsoc16#8 opened by thejmazz
discussion
VC with Bionode/JS Alpha Prototype
bionode/gsoc16#13 opened by thejmazz
discussion
Complete remaining week 1 tasks
bionode/gsoc16#11 opened by thejmazz
discussion
resolution scenarios (previous task vs fs)
bionode/bionode-watermill#10 opened by thejmazz
test
Resolve input from all tasks in join
bionode/bionode-watermill#35 opened by thejmazz
feature
Improve resolution of passed input
bionode/bionode-watermill#34 opened by thejmazz
enhancement
Catch Operation Finish
bionode/bionode-watermill#41 opened by thejmazz
feature
{ value: foo } type to just foo
bionode/bionode-watermill#33 opened by thejmazz
refactor
Correct usage guide on bionode-fasta cli
bionode/bionode-fasta#7 opened by cmdcolin
enhancement
A more idiomatic use of `into` operator
bionode/gsoc16#14 opened by pditommaso
discussion
Port task into redux actions
bionode/bionode-watermill#38 opened by thejmazz
enhancement
Basic genomic vcf workflow
bionode/bionode-watermill#28 opened by thejmazz
discussion
joins and parallels composability
bionode/bionode-watermill#13 opened by thejmazz
test
integrate once where applicable
bionode/bionode-watermill#32 opened by thejmazz
refactor
Async vs Sync Task creation
bionode/bionode-watermill#4 opened by thejmazz
discussion
resume option globally and per task
bionode/bionode-watermill#25 opened by thejmazz
enhancement
pass in custom validator functions
bionode/bionode-watermill#21 opened by thejmazz
feature
force rerun of all/specific task
bionode/bionode-watermill#24 opened by thejmazz
enhancement
file timestamp or checksum
bionode/bionode-watermill#23 opened by thejmazz
feature
null check validation
bionode/bionode-watermill#20 opened by thejmazz
feature
file existence validation
bionode/bionode-watermill#19 opened by thejmazz
feature
simple parallels
bionode/bionode-watermill#12 opened by thejmazz
test
simple joins
bionode/bionode-watermill#11 opened by thejmazz
test
Generalize traverse for resolving functions
bionode/bionode-watermill#8 opened by thejmazz
enhancement
Types
bionode/bionode-watermill#7 opened by thejmazz
discussion
Task Architecture
bionode/bionode-watermill#1 opened by thejmazz
discussion
Refactor out custom classes into vanilla objs
bionode/bionode-watermill#6 opened by thejmazz
enhancement
Passing output from last task into new task
bionode/bionode-watermill#5 opened by thejmazz
discussion
Check if outputted file is not null by default
bionode/bionode-watermill#9 opened by thejmazz
feature
Prevent Interference with Task Streams
bionode/bionode-watermill#3 opened by thejmazz
feature
VC with nextflow
bionode/gsoc16#7 opened by thejmazz
discussion
Week 2
bionode/gsoc16#12 opened by thejmazz
discussion
VC with snakemake
bionode/gsoc16#6 opened by thejmazz
discussion
VC with makefile
bionode/gsoc16#5 opened by thejmazz
discussion
Getting more done in GitHub with ZenHub
bionode/gsoc16#1 opened by thejmazz
discussion
Port away from event based stream
bionode/bionode-obo#24 opened by thejmazz
discussion
Pipe Stream into parser
bionode/bionode-obo#1 opened by thejmazz
enhancement
Include final stanza
bionode/bionode-obo#21 opened by thejmazz
bug
Handle multiple is_a's
bionode/bionode-obo#23 opened by thejmazz
bug
Fix EventEmitter2 problem on browsers
bionode/bionode-obo#22 opened by thejmazz
bug
add obo and quickgo to list of modules
bionode/bionode#32 opened by thejmazz
community
Currently down
bionode/try-bionode#2 opened by blahah
bug
Produce object stream
bionode/bionode-obo#3 opened by thejmazz
enhancement
Produce ndjson stream
bionode/bionode-obo#2 opened by thejmazz
enhancement
Cleaning and docs for 0.1.0 release
bionode/bionode-obo#19 opened by thejmazz
enhancement
Identify unrecognized stanzas
bionode/bionode-obo#11 opened by thejmazz
enhancement
Identify [Term], [Typedef], [Instance]
bionode/bionode-obo#4 opened by thejmazz
enhancement
Identify All record-type marks
bionode/bionode-obo#5 opened by thejmazz
enhancement
How to look up metadata for an SRR file
bionode/bionode-ncbi#17 opened by olgabot
question
Update package.json
bionode/bionode-vcf#1 opened by wookoouk
enhancement
Update package.json
bionode/bionode-vcf#2 opened by wookoouk
enhancement
Better docs
bionode/bionode-ncbi#15 opened by terfilip
enhancement
Implement efetch API
bionode/bionode-ncbi#10 opened by bmpvieira
feature
Efetch API
bionode/bionode-ncbi#14 opened by terfilip
feature
CLI JSON quick fix
bionode/bionode-ncbi#16 opened by terfilip
enhancement
User-friendly errors
bionode/bionode-ncbi#12 opened by terfilip
enhancement
Uncaught, unspecified "error" event
bionode/bionode-ncbi#13 opened by robsyme
invalid
N & X are not recognised as missing data
bionode/bionode-seq#2 opened by IsmailM
bug
Feature/travis versions and hooks
bionode/bionode-fastq#2 opened by bmpvieira
enhancement
Feature/standard style
bionode/bionode-fastq#4 opened by bmpvieira
enhancement
Add badges
bionode/bionode-fastq#3 opened by bmpvieira
enhancement
Add a Gitter chat badge to README.md
bionode-hack/bionode-example-dat-gasket#1 opened by gitter-badger
invalid
dont open stdin by default
bionode/bionode#15 opened by maxogden
bug
Remove duplicate dependency `tap-spec`
bionode/bionode#24 opened by c089
bug
windows install
bionode/bionode#20 opened by syzer
duplicate
waffle.io Badge
bionode/bionode#21 opened by waffle-iron
enhancement
waffle.io Badge
bionode/bionode#22 opened by waffle-iron
duplicate
pagination
bionode/bionode-ncbi#2 opened by maxogden
bug
fastq-dump a whole "SRP" project?
bionode/bionode-sra#2 opened by olgabot
question
download from protein database
bionode/bionode-ncbi#7 opened by olgabot
duplicate
curses.h missing on debian jessie
bionode/bionode#19 opened by fourpartswater
duplicate
command-line argument parsing error
bionode/bionode-ncbi#6 opened by blahah
duplicate
add JSONStream to package.json dependencies
bionode/bionode-template#1 opened by mkuzak
bug
Why restrict components to NPM?
bionode/bionode#14 opened by howardroark
discussion
Unexpected error when running 'bionode'
bionode/bionode-ncbi#9 opened by tseemann
duplicate
How do you define a bio-core?
bionode/bionode#11 opened by wilzbach
question
Get a sequence from a Genbank ID
bionode/bionode-ncbi#3 opened by audy
duplicate
Docker image for development and testing
bionode/bionode-sge#1 opened by bmpvieira
enhancement
Add a Gitter chat badge to README.md
bionode/bionode-fastq#1 opened by gitter-badger
community
parsers: blast
bionode/bionode#16 opened by wilzbach
community
Can't run on ZSH
bionode/bionode-sra#3 opened by olgabot
question
Updating the CheckType function
bionode/bionode-seq#1 opened by IsmailM
enhancement
switch from dld to nugget, upgrade some dependencies
bionode/bionode-ncbi#5 opened by maxogden
enhancement
retmax
bionode/bionode-ncbi#4 opened by vid
enhancement
Update README.md
bionode/bionode-fasta#5 opened by alanrice
community
changed biojs url to biojs.net
bionode/bionode#13 opened by wilzbach
community
Use Node.js streams
bionode/bionode-fasta#2 opened by alanrice
enhancement
Update README.md
bionode/bionode#12 opened by alanrice
community
Determine if sequence type is necessary
bionode/bionode-fasta#1 opened by alanrice
question
Allow stdin on CLI
bionode/bionode-fasta#3 opened by alanrice
enhancement
bionode-sra not in npm registry
bionode/bionode-sra#1 opened by olgabot
bug
Update checkSequenceType to follow IUPAC rules
bionode/bionode#8 opened by alanrice
enhancement
Support IUPAC
bionode/bionode#6 opened by bmpvieira
enhancement
add DEBUG=* logging support
bionode/bionode-ncbi#1 opened by maxogden
enhancement
Please make it AMD compliant.
bionode/bionode#1 opened by yeban
question
Add illustrative examples to docs
bionode/bionode#5 opened by alanrice
enhancement
Add a Bitdeli Badge to README
bionode/bionode#4 opened by bitdeli-chef
community