Ecosyste.ms: Issues

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GitHub / allenday/dataflow-genomics issues and pull requests

#51 - Bump htsjdk from 2.20.3 to 3.0.1 in /genomics-dataflow-core

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#50 - Bump commons-io from 2.6 to 2.7 in /genomics-dataflow-core

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#49 - Bump junit from 4.11 to 4.13.1 in /genomics-dataflow-core

Pull Request - State: open - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#48 - Bump junit from 4.11 to 4.13.1 in /giab-example

Pull Request - State: open - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#46 - add metada_generator. small fixes

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#45 - can't find bigquery table from vcf

Issue - State: open - Opened by Logan-Kang almost 5 years ago - 1 comment

#44 - ubam input

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#43 - 0417_giab varient calling error

Issue - State: closed - Opened by Logan-Kang almost 5 years ago - 4 comments

#42 - pom fixes, remove redundant code part

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#41 - add gzip input, some intermediate and finals results URI structure ch…

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#40 - small improvements and GIAB docs GCP setting tuning

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#39 - giab's variant caller error issue

Issue - State: closed - Opened by Logan-Kang almost 5 years ago - 4 comments

#38 - add variant calling GATk extension, pipeline parallelization improvements

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#37 - add fq as program argument

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#36 - Add source files extension as pipeline argument

Issue - State: open - Opened by pseveryn almost 5 years ago - 1 comment

#35 - fix aligner args

Pull Request - State: closed - Opened by pseveryn almost 5 years ago - 2 comments

#34 - remove redundant arg

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#33 - add fq support

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#32 - Questions about AlignAndPostProcessTransform.

Issue - State: closed - Opened by Logan-Kang almost 5 years ago - 17 comments

#31 - add aligner abstraction, BWA implementation, README extension

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#30 - Running Pipeline Command Issue

Issue - State: open - Opened by kyoobin10 almost 5 years ago - 1 comment

#29 - Does not have storage.objects.list access to dataflow-genomics-giab-demo

Issue - State: open - Opened by kyoobin10 almost 5 years ago - 1 comment

#28 - refactoring, add giab-example, docs for giab-example, base of main doc

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#27 - Adding GIAB NA12878 processing documentation

Issue - State: open - Opened by pseveryn almost 5 years ago - 1 comment

#26 - remove ValueProviders from refList and refDir

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#25 - sync dev with master

Pull Request - State: closed - Opened by pseveryn almost 5 years ago

#24 - Dev allenday

Pull Request - State: closed - Opened by allenday almost 5 years ago

#23 - move filesystem structure anomaly detection logic to core

Issue - State: open - Opened by allenday almost 5 years ago

#22 - remove hardcoded project ID PRJEB6180

Issue - State: open - Opened by allenday almost 5 years ago - 1 comment

#20 - SampleMetaDataTests - move this single test script elsewhere

Issue - State: open - Opened by allenday almost 5 years ago - 1 comment

#19 - remove `nanostream` from class namespaces

Issue - State: open - Opened by allenday almost 5 years ago - 6 comments

#18 - make huge refactoring connected with reference data providing improvements

Pull Request - State: closed - Opened by pseveryn almost 5 years ago - 2 comments

#17 - add new Instrument settings for minimap2, sra retriever changes

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#16 - add some changes after merging popgen projects

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#15 - Development

Pull Request - State: closed - Opened by allenday about 5 years ago

#14 - Files structure refactoring

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#13 - add cannabis-3k, rice-3k examples

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#12 - vcf to bq refactoring

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#11 - Development

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#10 - vcf to bq

Pull Request - State: closed - Opened by pseveryn about 5 years ago

#9 - Example => Sample, various other minor terminology fixes

Pull Request - State: closed - Opened by allenday over 5 years ago

#8 - add Sra parsing logic

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#7 - Deep variant added

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#6 - prepare to release to Maven Central

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#5 - prepare for Maven Central

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#4 - Added cloudbuild configuration for automated testing

Pull Request - State: closed - Opened by obsh over 5 years ago

#3 - Development

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#2 - add csv parsing logic

Pull Request - State: closed - Opened by pseveryn over 5 years ago

#1 - Update AlignService.java

Pull Request - State: closed - Opened by obsh over 5 years ago