Modular and universal bioinformatics
Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.
Project Board
Backlog 51
Highlight other projects using Bionode tools
bionode/bionode.github.io#6 opened by bmpvieira
community
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 5
User-friendly CLI
bionode/bionode#25 opened by c089
enhancement
Better handling of STDERR and STDOUT
bionode/bionode#41 opened by bmpvieira
enhancement
Improve global documentation generation and layout
bionode/bionode#27 opened by bmpvieira
enhancement
Add command line interface (CLI)
bionode/bionode-seq#5 opened by bmpvieira
feature
module links in readme are 404
bionode/bionode#30 opened by acthp
community
In Progress 6
geo is not searchable
bionode/bionode-ncbi#20 opened by lorenzorietti
enhancementin progress
Code of Conduct
bionode/bionode#38 opened by bmpvieira
community
Follow the JavaScript Standard style
bionode/bionode#26 opened by bmpvieira
chore
Styleguide for tagging
bionode/bionode#39 opened by bmpvieira
chore
Done 143
Roadmap
bionode/bionode#35 opened by bmpvieira
discussion
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/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