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Modular and universal bioinformatics
Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.
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Project Board
Backlog70
general question
bionode/bionode-vcf#7 opened bymatthdsm
Execution of a pipeline following other pipeline
bionode/bionode-watermill#82 opened bytiagofilipe12
discussion
Through tasks not properly logging
bionode/bionode-watermill#81 opened bytiagofilipe12
discussion
Improve validators over input/output files
bionode/bionode-watermill#80 opened bytiagofilipe12
discussionfeature
Streaming Between Tasks
bionode/bionode-watermill#79 opened bythejmazz
discussionfeature
Tasks as npm modules
bionode/bionode-watermill#78 opened bytiagofilipe12
discussion
Improvements to visualization tool
bionode/bionode-watermill#77 opened bytiagofilipe12
enhancement
CLI needs testing
bionode/bionode-seq#8 opened bybmpvieira
test
"task binding" without hardcoded file suffixes
bionode/bionode-watermill#66 opened bythejmazz
discussion
Refactor task definition
bionode/bionode-watermill#75 opened bytiagofilipe12
refactor
Refactor pipeline parsing
bionode/bionode-watermill#74 opened bytiagofilipe12
refactor
Personas and Pathways - plan for your project users and their participation
bionode/bionode#37 opened bybmpvieira
communitymozsprint
Add support for cluster computing
bionode/bionode-watermill#63 opened bytiagofilipe12
enhancementfeature
Added a .travis.yml file.
bionode/bionode-scripts#3 opened byStuntsPT
enhancementmozsprint
Added a .travis.yml file.
bionode/bionode-blast#3 opened byStuntsPT
enhancementmozsprint
Added .travis.yml node.js environment. Fixes #2.
bionode/events#3 opened byStuntsPT
enhancementmozsprint
Added .travis.yml node.js environment. Fixes #2.
bionode/bionode-quickgo#3 opened byStuntsPT
enhancementmozsprint
Add a .travis.yml file with Node environment
bionode/events#2 opened bybmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-scripts#2 opened bybmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-blast#2 opened bybmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/gsoc16#16 opened bybmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/try-bionode#4 opened bybmpvieira
mozsprinttest
Add a .travis.yml file with Node environment
bionode/bionode-quickgo#2 opened bybmpvieira
mozsprinttest
Convert from wrapper to native module
bionode/bionode-sam#3 opened bybmpvieira
featuremozsprint
consider renaming this module
bionode/fasta-parser#3 opened bytiagofilipe12
discussion
Integrate nodestream
bionode/bionode-watermill#46 opened bythejmazz
discussionmozsprint
bionode-seq features as Atom.io plugin
bionode/bionode-seq#4 opened byilevantis
featuremozsprint
Common Workflow Language (CWL) support?
bionode/bionode-watermill#45 opened byolgabot
CWLdiscussionmozsprint
flag to allow input resolution to fallback to cwd
bionode/bionode-watermill#44 opened bythejmazz
enhancement
better logs when input is not resolved
bionode/bionode-watermill#43 opened bythejmazz
enhancement
Custom file validator over output object
bionode/bionode-watermill#42 opened bythejmazz
feature
json schema validator on input, output, action stream
bionode/bionode-watermill#39 opened bythejmazz
enhancementvalidators
Trinity Pipeline
bionode/bionode-watermill#37 opened bythejmazz
examples
Parallelize BAM chunks
bionode/bionode-watermill#36 opened bythejmazz
examples
Basic CLI
bionode/bionode-watermill#31 opened bythejmazz
feature
Advanced genomic vcf workflow
bionode/bionode-watermill#29 opened bythejmazz
enhancement
Test Reentrancy
bionode/bionode-watermill#27 opened bythejmazz
test
tee stream to file
bionode/bionode-watermill#26 opened bythejmazz
feature
File Validation
bionode/bionode-watermill#22 opened bythejmazz
epicfeature
stream search results, filter down to IDs, run pipeline on each ID
bionode/bionode-watermill#17 opened bythejmazz
examples
transform task
bionode/bionode-watermill#15 opened bythejmazz
test
Parallelization?
bionode/bionode-sra#4 opened byolgabot
question
ES6 Discussion
bionode/bionode#33 opened bythejmazz
discussion
Remove zlib dependency, replace with core Node api
bionode/bionode-fasta#6 opened bythejmazz
enhancement
Integrate with OBO 1.2 spec
bionode/bionode-obo#7 opened bythejmazz
enhancement
Identify all stanza, tag types
bionode/bionode-obo#6 opened bythejmazz
enhancement
Stanza parser
bionode/bionode-obo#20 opened bythejmazz
test
[Typdef] cannot have union_of, intersection_of, disjoint_from
bionode/bionode-obo#13 opened bythejmazz
enhancement
Handle unrecognized tags
bionode/bionode-obo#16 opened bythejmazz
enhancement
Handle trailing modifiers
bionode/bionode-obo#9 opened bythejmazz
enhancement
Handle escape characters
bionode/bionode-obo#10 opened bythejmazz
enhancement
Handle dangling references
bionode/bionode-obo#17 opened bythejmazz
enhancement
Handle comments
bionode/bionode-obo#8 opened bythejmazz
enhancement
Define/follow serializer conventions
bionode/bionode-obo#18 opened bythejmazz
enhancement
Define spec requirements with json
bionode/bionode-obo#15 opened bythejmazz
enhancement
Check for id, name, instance_of in [Instance]
bionode/bionode-obo#14 opened bythejmazz
enhancement
Check for id, name in [Term] stanza
bionode/bionode-obo#12 opened bythejmazz
enhancement
Enhancement: more lessons!
bionode/biohacker#1 opened by100ideas
enhancementmozsprint
RequireBin FLAGRANT SYSTEM ERROR
bionode/bionode#31 opened byshotlom
bug
Change tests engine from chai to tape for compatibility with main bionode module
bionode/bionode-fastq#5 opened bybmpvieira
choremozsprint
Change tests engine from 'assert' to 'tape' for compatibility with main bionode module
bionode/bionode-gff#1 opened bybmpvieira
choremozsprint
Make Docker image and users /home more lightweight
bionode/try-bionode#1 opened bybmpvieira
enhancement
Write wrapper around qsub
bionode/bionode-sge#2 opened bybmpvieira
featurehelp wanted
Issues with modules that require binaries (wrappers)
bionode/bionode#29 opened bybmpvieira
discussionhelp wanted
Autogenerate module template
bionode/bionode#23 opened bybmpvieira
enhancementmozsprint
sam parser in bionode
bionode/bionode#17 opened bywilzbach
enhancementhelp wanted
Refactor to be more like other bionode modules
bionode/bionode-bbi#1 opened bybmpvieira
enhancementhelp wanted
Add documentation, and more info to README.md
bionode/bionode-bbi#2 opened bybmpvieira
documentationhelp wanted
Add tests
bionode/bionode-sam#1 opened bybmpvieira
enhancement
Add documentation
bionode/bionode-sam#2 opened bybmpvieira
enhancement
Next11
Add insight dependency to anonymously report usage metrics
bionode/bionode-watermill#87 opened bybmpvieira
enhancement
Refactoring to use stream modules
bionode/bionode-fastq#7 opened bytiagofilipe12
enhancementmozsprint
Output some warning to terminal when there is no output
bionode/bionode-ncbi#38 opened bytiagofilipe12
ux
benchmark watermill
bionode/GSoC17#3 opened bytiagofilipe12
User-friendly CLI
bionode/bionode#25 opened byc089
enhancement
Better handling of STDERR and STDOUT
bionode/bionode#41 opened bybmpvieira
enhancement
Improve global documentation generation and layout
bionode/bionode#27 opened bybmpvieira
enhancement
Modularize lib structure.
bionode/bionode-ncbi#34 opened byIstar-Eldritch
enhancement
Follow the JavaScript Standard style
bionode/bionode#26 opened bybmpvieira
choremozsprint
Styleguide for tagging
bionode/bionode#39 opened bybmpvieira
choremozsprint
Add insight dependency to anonymously report usage metrics
bionode/bionode#34 opened bybmpvieira
choremozsprint
In Progress5
NPM release to include CLI
bionode/bionode-fastq#11 opened bythejmazz
chore
Multiple inputs for a task
bionode/bionode-watermill#65 opened bytiagofilipe12
enhancement
Output file matches when defining a task
bionode/bionode-watermill-tutorial#3 opened byODiogoSilva
enhancementquestion
Add considerations on the use of patterns and pipes
bionode/GSoC17#4 opened bytiagofilipe12
discussion
Simple usage tutorial
bionode/bionode-watermill#49 opened bytiagofilipe12
documentationmozsprint
Done252
Netlify
bionode/github-project-public#5 opened byIsmailM
enhancement
Netlify
bionode/doc.bionode.io#4 opened byIsmailM
enhancement
update internal links
bionode/bionode.io#16 opened byIsmailM
enhancement
Replace jq dependency with npm's json, and change code
bionode/bionode.io#14 opened bybmpvieira
chore
Host using Github + Netlify
bionode/bionode.io#12 opened byIsmailM
enhancement
Update deploy method
bionode/bionode.io#15 opened byIsmailM
enhancement
Ssl
bionode/bionode.io#13 opened byIsmailM
feature
Change on the behavior of d3 visualization
bionode/bionode-watermill#86 opened bytiagofilipe12
documentationux
Docs update - fixing syntax errors
bionode/bionode-watermill#85 opened bytiagofilipe12
documentation
Docs update
bionode/bionode-watermill#84 opened bytiagofilipe12
documentation
Fix README header rendering
bionode/bionode-fasta#10 opened byerictleung
chore
Image at the bottom of readme file is broken.
bionode/bionode-sam#5 opened byyeban
documentationmozsprint
Standardization
bionode/bionode-sam#6 opened byStuntsPT
enhancementmozsprint
Standardization
bionode/bionode-gff#3 opened byStuntsPT
enhancementmozsprint
Standardization
bionode/bionode-vcf#6 opened byStuntsPT
enhancementmozsprint
Unit tests for task orchestration
bionode/bionode-watermill#18 opened bythejmazz
test
complex join, parallels, forking
bionode/bionode-watermill#16 opened bythejmazz
test
Merge Develop into Master in preparation for 1.0.0
bionode/bionode-watermill#83 opened bythejmazz
enhancement
Docs update
bionode/bionode-watermill#76 opened bytiagofilipe12
documentation
Example Pipelines
bionode/bionode-watermill#30 opened bythejmazz
enhancementepic
Add command line interface (CLI)
bionode/bionode-seq#5 opened bybmpvieira
feature
CLI (fixes #5)
bionode/bionode-seq#7 opened byColelyman
feature
Add MIT LICENSE file and change it from ISC in package.json
bionode/github-project-public#3 opened bybmpvieira
legalmozsprint
Added a license file.
bionode/github-project-public#4 opened byStuntsPT
enhancementmozsprint
Standardized README.md
bionode/bionode-fastq#9 opened byStuntsPT
enhancement
Corrected a typo and improved line spacings.
bionode/bionode-ncbi#37 opened byStuntsPT
enhancementmozsprint
Check if file is empty
bionode/bionode-watermill#51 opened bytiagofilipe12
bugmozsprint
simple forking
bionode/bionode-watermill#14 opened bythejmazz
test
Add a .travis.yml file with Node environment
bionode/bionode-obo#26 opened bybmpvieira
mozsprinttest
Added a .travis.yml file.
bionode/bionode-obo#27 opened byStuntsPT
enhancementmozsprint
Add another test for fork within fork wrapped in join
bionode/bionode-watermill#73 opened bytiagofilipe12
test
Installation failed - sra toolkit permanently moved
bionode/bionode-sra#8 opened byBrettHoutz
bug
Standardization
bionode/bionode-sra#7 opened byStuntsPT
enhancementmozsprint
[Snyk] Fix for 1 vulnerable dependency path
bionode/bionode-watermill#68 opened bysnyk-bot
security
Pipeline Graph (DAG) Visualization
bionode/bionode-watermill#50 opened bythejmazz
featuremozsprint
geo is not searchable
bionode/bionode-ncbi#20 opened bylorenzorietti
enhancementmozsprint
Do the db filter at lib level
bionode/bionode-ncbi#33 opened byIstar-Eldritch
featuremozsprint
CLI implementation
bionode/bionode-fastq#8 opened bytiagofilipe12
enhancementmozsprint
CLI
bionode/bionode-fastq#10 opened byColelyman
enhancement
added task.name to uid generator
bionode/bionode-watermill#69 opened bytiagofilipe12
bug
Going deeper on fork orchestration
bionode/bionode-watermill#72 opened bytiagofilipe12
enhancement
Orchestrators tests
bionode/bionode-watermill#71 opened bythejmazz
test
Sanitization and tidy up of Dockerfile
bionode/bionode-watermill-tutorial#4 opened byODiogoSilva
enhancement
Orchestrators refactoring and fork handling other orchestrators
bionode/bionode-watermill#70 opened bytiagofilipe12
refactor
Added gitbooks entries
bionode/GSoC17#5 opened bytiagofilipe12
documentation
edits to two-mappers pipeline and removed of redundant defaultTask
bionode/bionode-watermill#67 opened bytiagofilipe12
enhancement
Added operation command to graphson
bionode/bionode-watermill#64 opened bytiagofilipe12
enhancement
Implemented a graph visualization
bionode/bionode-watermill#62 opened bytiagofilipe12
feature
implemented redux-logger given an environmental variable
bionode/bionode-watermill#61 opened bytiagofilipe12
enhancement
Graph file
bionode/bionode-watermill#60 opened bytiagofilipe12
enhancement
Summary file
bionode/bionode-watermill#57 opened bytiagofilipe12
enhancement
Transfered experimental branch for development of graph
bionode/bionode-watermill#59 opened bytiagofilipe12
enhancement
Fixed issue with logging of task name to stdout
bionode/bionode-watermill#58 opened bytiagofilipe12
bug
Adds a new example pipeline and edits existing example pipeline
bionode/bionode-watermill#53 opened bytiagofilipe12
examples
Add a Gitter chat badge to README.md
bionode/GSoC17#2 opened bygitter-badger
community
Explain template literals
bionode/bionode-watermill-tutorial#1 opened bytiagofilipe12
enhancement
Tutorial 1 - Input/output declaration
bionode/bionode-watermill-tutorial#2 opened bybfrgoncalves
enhancement
Updated docker related links and added link to tutorial in README
bionode/bionode-watermill#56 opened bytiagofilipe12
documentation
Added a tutorial on how to run "two-mappers" example
bionode/bionode-watermill#55 opened bytiagofilipe12
documentation
add license type
bionode/bionode-watermill#54 opened bytiagofilipe12
legal
only push when not a PR
bionode/bionode.io#11 opened byIsmailM
bug
Travis pushes to the live website for all PR from branches
bionode/bionode.io#10 opened byIsmailM
bug
Add obf
bionode/bionode.io#9 opened byIsmailM
community
Mozilla's Global Sprint (June 1st and 2nd 2017)
bionode/bionode#44 opened bybmpvieira
communitymozsprint
Roadmap
bionode/bionode#42 opened bybmpvieira
discussionmozsprint
Recognise all kinds of contributions
bionode/bionode#43 opened bybmpvieira
communitymozsprint
How can be a pipeline extended to deal with multiple samples?
bionode/bionode-watermill#47 opened byzhangzhen
mozsprintquestion
Standardization
bionode/bionode#45 opened byStuntsPT
enhancementmozsprint
Code of Conduct
bionode/bionode#38 opened bybmpvieira
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/events#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-bbi#3 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/biohacker#2 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-sam#4 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-examples#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-go#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-seq#6 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/docker-browser-server#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-flow#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-gff#2 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-fastq#6 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-quickgo#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-obo#25 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/try-bionode#3 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/gsoc16#15 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-scripts#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-blast#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-vcf#5 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode.io#8 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/github-project-public#2 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/get-bionode#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-sra#6 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-fasta#9 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/doc.bionode.io#3 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-watermill#52 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/GSoC17#1 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-bwa#2 opened byayangromano
communitymozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-template#3 opened byayangromano
communitymozsprint
Standardize
bionode/bionode-template#2 opened byStuntsPT
enhancementmozsprint
Create CODE_OF_CONDUCT.md
bionode/bionode-ncbi#36 opened byayangromano
communitymozsprint
Standardization
bionode/bionode-bwa#1 opened byStuntsPT
enhancementmozsprint
module links in readme are 404
bionode/bionode#30 opened byacthp
communitymozsprint
Standardization
bionode/bionode-ncbi#35 opened byStuntsPT
enhancementmozsprint
Highlight other projects using Bionode tools
bionode/bionode.io#6 opened bybmpvieira
community
Add Users and Acknowledgement sections
bionode/bionode.io#7 opened byIsmailM
community
correct path to home folder
bionode/bionode-watermill#48 opened bytiagofilipe12
bug
Responsive columns
bionode/github-project-public#1 opened byIsmailM
enhancement
fix typos
bionode/doc.bionode.io#2 opened byIsmailM
documentation
Fix bionode-ncbi example
bionode/doc.bionode.io#1 opened byerictleung
documentation
Old Roadmap
bionode/bionode#35 opened bybmpvieira
discussion
make the font-size larger (1.4rem) in the about section
bionode/bionode.io#5 opened byIsmailM
enhancement
Update CONTRIBUTE.md
bionode/bionode#36 opened bybmpvieira
community
Error handling when NCBI connection is lost
bionode/bionode-ncbi#29 opened bytiagofilipe12
discussion
Download the GFF file of the Cycas taitungensis mitochondrion
bionode/bionode-ncbi#11 opened bysjackman
enhancement
User-friendly CLI
bionode/bionode-ncbi#31 opened bybmpvieira
enhancement
Better CLI, this fixes #31, #29, #20 and #11
bionode/bionode-ncbi#32 opened bybmpvieira
enhancement
Prevent progress bar from starting if file already exists
bionode/bionode-ncbi#30 opened bytiagofilipe12
ux
add events section to the website
bionode/bionode.io#4 opened byIsmailM
community
update website content
bionode/bionode.io#3 opened byIsmailM
chore
Generate team and contributors for homepage automatically from GitHub.
bionode/bionode.io#1 opened bybmpvieira
community
Generate team and contributors for homepage automatically from GitHub...
bionode/bionode.io#2 opened byIsmailM
community
Update on docs, removing a useless comment
bionode/bionode-ncbi#28 opened bytiagofilipe12
documentation
We need a smaller assembly from NCBI for testing
bionode/bionode-ncbi#24 opened bybmpvieira
test
Add smaller download assembly for testing and fix #24
bionode/bionode-ncbi#27 opened bytiagofilipe12
test
Git rid of git-lfs
bionode/bionode-ncbi#25 opened bybmpvieira
test
Remove git-lfs
bionode/bionode-ncbi#26 opened bybmpvieira
test
download in the examples printing too much info
bionode/bionode-ncbi#22 opened bytiagofilipe12
ux
Progress bar
bionode/bionode-ncbi#23 opened bytiagofilipe12
ux
Timeline
bionode/bionode-watermill#2 opened bythejmazz
discussion
v0.2.x
bionode/bionode-watermill#40 opened bythejmazz
discussion
Make project board public
bionode/bionode#40 opened bybmpvieira
community
Upkeep
bionode/fasta-parser#2 opened byRudani
chore
Raise error on failed parsing and ignore empty stream
bionode/fasta-parser#1 opened bydrpowell
enhancement
Fix code to follow StandardJS style guide
bionode/bionode-fasta#8 opened byRudani
chore
Fix tests (#18) and mocking NCBI API
bionode/bionode-ncbi#21 opened bybmpvieira
bug
Tests are broken because of NCBI side metadata changes (again)
bionode/bionode-ncbi#18 opened bybmpvieira
bug
Add a Gitter chat badge to README.md
bionode-hack/bionodered#1 opened bygitter-badger
enhancement
Formatting fix and https fix for sra toolkit download
bionode/bionode-sra#5 opened byamanjeev
bug
Dependency removal (fs)
bionode/bionode-vcf#4 opened byamblina
bug
rna_from_genomic instead of genomic.fna
bionode/bionode-ncbi#19 opened bythejmazz
bug
Papers
bionode/gsoc16#10 opened bythejmazz
discussion
Google Summer of Code 2015
bionode/bionode#28 opened bybmpvieira
community
Update index.js
bionode/bionode-vcf#3 opened bywookoouk
deprecated
Week 1
bionode/gsoc16#9 opened bythejmazz
discussion
VC workflows comparison
bionode/gsoc16#8 opened bythejmazz
discussion
VC with Bionode/JS Alpha Prototype
bionode/gsoc16#13 opened bythejmazz
discussion
Complete remaining week 1 tasks
bionode/gsoc16#11 opened bythejmazz
discussion
resolution scenarios (previous task vs fs)
bionode/bionode-watermill#10 opened bythejmazz
test
Resolve input from all tasks in join
bionode/bionode-watermill#35 opened bythejmazz
feature
Improve resolution of passed input
bionode/bionode-watermill#34 opened bythejmazz
enhancement
Catch Operation Finish
bionode/bionode-watermill#41 opened bythejmazz
feature
{ value: foo } type to just foo
bionode/bionode-watermill#33 opened bythejmazz
refactor
Correct usage guide on bionode-fasta cli
bionode/bionode-fasta#7 opened bycmdcolin
enhancement
A more idiomatic use of `into` operator
bionode/gsoc16#14 opened bypditommaso
discussion
Port task into redux actions
bionode/bionode-watermill#38 opened bythejmazz
enhancement
Basic genomic vcf workflow
bionode/bionode-watermill#28 opened bythejmazz
discussion
joins and parallels composability
bionode/bionode-watermill#13 opened bythejmazz
test
integrate once where applicable
bionode/bionode-watermill#32 opened bythejmazz
refactor
Async vs Sync Task creation
bionode/bionode-watermill#4 opened bythejmazz
discussion
resume option globally and per task
bionode/bionode-watermill#25 opened bythejmazz
enhancement
pass in custom validator functions
bionode/bionode-watermill#21 opened bythejmazz
feature
force rerun of all/specific task
bionode/bionode-watermill#24 opened bythejmazz
enhancement
file timestamp or checksum
bionode/bionode-watermill#23 opened bythejmazz
feature
null check validation
bionode/bionode-watermill#20 opened bythejmazz
feature
file existence validation
bionode/bionode-watermill#19 opened bythejmazz
feature
simple parallels
bionode/bionode-watermill#12 opened bythejmazz
test
simple joins
bionode/bionode-watermill#11 opened bythejmazz
test
Generalize traverse for resolving functions
bionode/bionode-watermill#8 opened bythejmazz
enhancement
Types
bionode/bionode-watermill#7 opened bythejmazz
discussion
Task Architecture
bionode/bionode-watermill#1 opened bythejmazz
discussion
Refactor out custom classes into vanilla objs
bionode/bionode-watermill#6 opened bythejmazz
enhancement
Passing output from last task into new task
bionode/bionode-watermill#5 opened bythejmazz
discussion
Check if outputted file is not null by default
bionode/bionode-watermill#9 opened bythejmazz
feature
Prevent Interference with Task Streams
bionode/bionode-watermill#3 opened bythejmazz
feature
VC with nextflow
bionode/gsoc16#7 opened bythejmazz
discussion
Week 2
bionode/gsoc16#12 opened bythejmazz
discussion
VC with snakemake
bionode/gsoc16#6 opened bythejmazz
discussion
VC with makefile
bionode/gsoc16#5 opened bythejmazz
discussion
VC with bionode-ncbi+tools (bash) with filtering
bionode/gsoc16#4 opened bythejmazz
discussion
Getting more done in GitHub with ZenHub
bionode/gsoc16#1 opened bythejmazz
discussion
Collate notes from 4 NGS VC papers into summary+questions
bionode/gsoc16#3 opened bythejmazz
discussion
Run simple bionode-ncbi + tools VC bash script
bionode/gsoc16#2 opened bythejmazz
discussion
Port away from event based stream
bionode/bionode-obo#24 opened bythejmazz
discussion
Pipe Stream into parser
bionode/bionode-obo#1 opened bythejmazz
enhancement
Include final stanza
bionode/bionode-obo#21 opened bythejmazz
bug
Handle multiple is_a's
bionode/bionode-obo#23 opened bythejmazz
bug
Fix EventEmitter2 problem on browsers
bionode/bionode-obo#22 opened bythejmazz
bug
add obo and quickgo to list of modules
bionode/bionode#32 opened bythejmazz
community
Currently down
bionode/try-bionode#2 opened byblahah
bug
Produce object stream
bionode/bionode-obo#3 opened bythejmazz
enhancement
Produce ndjson stream
bionode/bionode-obo#2 opened bythejmazz
enhancement
Cleaning and docs for 0.1.0 release
bionode/bionode-obo#19 opened bythejmazz
enhancement
Identify unrecognized stanzas
bionode/bionode-obo#11 opened bythejmazz
enhancement
Identify [Term], [Typedef], [Instance]
bionode/bionode-obo#4 opened bythejmazz
enhancement
Identify All record-type marks
bionode/bionode-obo#5 opened bythejmazz
enhancement
How to look up metadata for an SRR file
bionode/bionode-ncbi#17 opened byolgabot
question
Update package.json
bionode/bionode-vcf#1 opened bywookoouk
enhancement
Update package.json
bionode/bionode-vcf#2 opened bywookoouk
enhancement
Better docs
bionode/bionode-ncbi#15 opened byterfilip
enhancement
Implement efetch API
bionode/bionode-ncbi#10 opened bybmpvieira
feature
Efetch API
bionode/bionode-ncbi#14 opened byterfilip
feature
CLI JSON quick fix
bionode/bionode-ncbi#16 opened byterfilip
enhancement
User-friendly errors
bionode/bionode-ncbi#12 opened byterfilip
enhancement
Provide a user-friendly error when unable to access NCBI servers
bionode/bionode-ncbi#8 opened bybmpvieira
enhancement
Uncaught, unspecified "error" event
bionode/bionode-ncbi#13 opened byrobsyme
invalid
ignore 'N' & 'X' within the CheckType function
bionode/bionode-seq#3 opened byIsmailM
bug
N & X are not recognised as missing data
bionode/bionode-seq#2 opened byIsmailM
bug
Feature/travis versions and hooks
bionode/bionode-fastq#2 opened bybmpvieira
enhancement
Feature/standard style
bionode/bionode-fastq#4 opened bybmpvieira
enhancement
Add badges
bionode/bionode-fastq#3 opened bybmpvieira
enhancement
Add a Gitter chat badge to README.md
bionode-hack/bionode-example-dat-gasket#1 opened bygitter-badger
invalid
dont open stdin by default
bionode/bionode#15 opened bymaxogden
bug
Remove duplicate dependency `tap-spec`
bionode/bionode#24 opened byc089
bug
windows install
bionode/bionode#20 opened bysyzer
duplicate
waffle.io Badge
bionode/bionode#21 opened bywaffle-iron
enhancement
waffle.io Badge
bionode/bionode#22 opened bywaffle-iron
duplicate
pagination
bionode/bionode-ncbi#2 opened bymaxogden
bug
fastq-dump a whole "SRP" project?
bionode/bionode-sra#2 opened byolgabot
question
download from protein database
bionode/bionode-ncbi#7 opened byolgabot
duplicate
curses.h missing on debian jessie
bionode/bionode#19 opened byfourpartswater
duplicate
curl not installed by default on debian machines
bionode/bionode#18 opened byfourpartswater
duplicate
command-line argument parsing error
bionode/bionode-ncbi#6 opened byblahah
duplicate
add JSONStream to package.json dependencies
bionode/bionode-template#1 opened bymkuzak
bug
Why restrict components to NPM?
bionode/bionode#14 opened byhowardroark
discussion
Unexpected error when running 'bionode'
bionode/bionode-ncbi#9 opened bytseemann
duplicate
How do you define a bio-core?
bionode/bionode#11 opened bywilzbach
question
How do we manage to bundle the documentation of all plugins into a Biogems website?
bionode/bionode#10 opened bywilzbach
enhancement
Get a sequence from a Genbank ID
bionode/bionode-ncbi#3 opened byaudy
duplicate
Docker image for development and testing
bionode/bionode-sge#1 opened bybmpvieira
enhancement
Collaboration with BioJS (same module system and package manager)
bionode/bionode#9 opened bybmpvieira
discussion
Add a Gitter chat badge to README.md
bionode/bionode-fastq#1 opened bygitter-badger
community
parsers: blast
bionode/bionode#16 opened bywilzbach
community
Can't run on ZSH
bionode/bionode-sra#3 opened byolgabot
question
Updating the CheckType function
bionode/bionode-seq#1 opened byIsmailM
enhancement
switch from dld to nugget, upgrade some dependencies
bionode/bionode-ncbi#5 opened bymaxogden
enhancement
retmax
bionode/bionode-ncbi#4 opened byvid
enhancement
Update README.md
bionode/bionode-fasta#5 opened byalanrice
community
changed biojs url to biojs.net
bionode/bionode#13 opened bywilzbach
community
Use Node.js streams
bionode/bionode-fasta#2 opened byalanrice
enhancement
Update README.md
bionode/bionode#12 opened byalanrice
community
Determine if sequence type is necessary
bionode/bionode-fasta#1 opened byalanrice
question
Allow stdin on CLI
bionode/bionode-fasta#3 opened byalanrice
enhancement
bionode-sra not in npm registry
bionode/bionode-sra#1 opened byolgabot
bug
Decide on output format for interoperability between parsers
bionode/bionode-fasta#4 opened byalanrice
discussion
Update checkSequenceType to follow IUPAC rules
bionode/bionode#8 opened byalanrice
enhancement
Support IUPAC
bionode/bionode#6 opened bybmpvieira
enhancement
Support IUPAC notation in checkSequenceType function
bionode/bionode#7 opened byalanrice
enhancement
add DEBUG=* logging support
bionode/bionode-ncbi#1 opened bymaxogden
enhancement
please could you implement a function to find longest orf?
bionode/bionode#3 opened byyeban
feature
can we similarly have a function to find detect non canonical translation sites?
bionode/bionode#2 opened byyeban
feature
Please make it AMD compliant.
bionode/bionode#1 opened byyeban
question
Add illustrative examples to docs
bionode/bionode#5 opened byalanrice
enhancement
Add a Bitdeli Badge to README
bionode/bionode#4 opened bybitdeli-chef
community
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