117
2015-11-13 Lightning sprint
 
2015-11-13
2015-10-23
  • Update Lightning v0.1 Specifications
    7455
    Lightning
    43
    Story
    6
    Closed
    5
    1.0
    1.0
    117
    -c-a
    43
  • Document Sprite Annotation Server
    7296
    Lightning
    43
    Story
    6
    Closed
    5
    1.0
    1.0
    117
    -c-a
    43
  • Implement upload Genome to Lightning Pipeline
    3535
    Lightning
    43
    Story
    6
    Closed
    5
    117
    -c-a
    43
  • CGF of 1kg and PGP for paths 2c5 and 247 (cont.)
    7427
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    117
    -c-a
    43
118
2015-12-04 Lightning sprint
 
2015-12-04
2015-11-13
  • gVCF to FASTJ converter
    6228
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    118
    -c-a
    43
  • Scale up CGF library creation to be run on Arvados for whole genome for all 433 1kg and 174+ PGP samples.
    7383
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    118
    -c-a
    43
  • Implement annotation on Tile Library
    7267
    Lightning
    43
    Story
    6
    New
    1
    3.0
    3.0
    118
    -c-a
    43
  • Test PCA for tiled genomes that handles missing data
    7316
    Lightning
    43
    Story
    6
    Closed
    5
    118
    -c-a
    43
  • gVCF/VCF Tyler Implementation
    7489
    Lightning
    43
    Story
    6
    New
    1
    1.0
    1.0
    118
    -c-a
    43
  • Annotate 680 Genomes Library
    7300
    Lightning
    43
    Story
    6
    New
    1
    3.0
    3.0
    118
    -c-a
    43
  • Clean up lightning git repository
    6703
    Lightning
    43
    Story
    6
    Closed
    5
    2.5
    2.5
    118
    -c-a
    43
  • Explain Lightning API Decisions and add examples (#5339)
    5587
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    118
    -c-a
    43
163
Lightning Sprint (2017-05-15 to 2017-05-29)
 
2017-05-29
2017-05-15
  • Tile library versioning specification and tool
    11676
    Lightning
    43
    Story
    6
    New
    1
    3.0
    3.0
    163
    -c-a
    43
  • Add library and genome versioning to CGF format and cgft tool
    11677
    Lightning
    43
    Story
    6
    New
    1
    1.0
    1.0
    163
    -c-a
    43
  • Extend CGF to include genotyping
    11673
    Lightning
    43
    Story
    6
    In Progress
    2
    1.0
    1.0
    163
    -c-a
    43
  • Convert openSNP genotyping data to CGF
    11674
    Lightning
    43
    Story
    6
    In Progress
    2
    4.0
    4.0
    163
    -c-a
    43
  • Convert 650+ CGF files to new CGFv3
    11671
    Lightning
    43
    Story
    6
    Closed
    5
    4.0
    4.0
    163
    -c-a
    43
114
Future sprints (Lightning)
 
2020-10-13
2020-09-29
  • Lightning deployment plan / Uploading data specifications
    5056
    Lightning
    43
    Story
    6
    Closed
    5
    0.5
    0.5
    114
    -c-a
    43
  • gVCF/VCF Tyler Specification
    7488
    Lightning
    43
    Story
    6
    Closed
    5
    1.0
    1.0
    114
    -c-a
    43
  • Implement Annotation database in Sprite
    5002
    Lightning
    43
    Story
    6
    New
    1
    114
    -c-a
    43
  • align2gvcf test suite
    5983
    Lightning
    43
    Story
    6
    Closed
    5
    2.0
    2.0
    114
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/vcf API call
    7441
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/gvcf API call
    5334
    Lightning
    43
    Story
    6
    New
    1
    114
    -c-a
    43
  • [API] Implement GET /callsets/{callset-name}/tile-variants
    5329
    Lightning
    43
    Story
    6
    New
    1
    2.0
    2.0
    114
    -c-a
    43
  • [API] Implement "GET /assemblies" API Calls
    5470
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • [API] Implement filtering on API calls
    5331
    Lightning
    43
    Story
    6
    New
    1
    1.0
    1.0
    114
    -c-a
    43
  • [API] [Documentation] Specify how to find the variants in a gene
    5335
    Lightning
    43
    Story
    6
    New
    1
    114
    -c-a
    43
  • [Documentation] [Sprite] [API] Specify API Calls and Database for phenotypes in Sprite
    5332
    Lightning
    43
    Story
    6
    New
    1
    2.0
    2.0
    114
    -c-a
    43
  • [Documentation] Specify batch API-like queries
    5330
    Lightning
    43
    Story
    6
    New
    1
    2.0
    2.0
    114
    -c-a
    43
  • Ensure GFF to FASTJ in Lightning git repo
    3538
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • Create CGF Files and Lantern Server for 1000 Genomes WGS
    5001
    Lightning
    43
    Story
    6
    Closed
    5
    5.0
    5.0
    114
    -c-a
    43
  • FASTQ to FASTJ Implementation
    3536
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • CGF path vectors have no-calls on end
    5302
    Lightning
    43
    Bug
    1
    Closed
    5
    2.0
    2.0
    114
    -c-a
    43
  • [gff2fj] Does not correctly label no-calls at end of cytogenetic band
    5903
    Lightning
    43
    Bug
    1
    Closed
    5
    114
    -c-a
    43
  • [gff2fj] Add in error checks to check common errors and do sanity checks on resulting FastJ files
    5904
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • Implement ProbabilisticPCA on Tiled Genomes
    6653
    Lightning
    43
    Story
    6
    New
    1
    2.5
    2.5
    114
    -c-a
    43
  • Specify/Document how to use Lightning for family analysis
    5336
    Lightning
    43
    Story
    6
    New
    1
    114
    -c-a
    43
  • Specify GA4GH API Implementation with Lightning
    5371
    Lightning
    43
    Story
    6
    New
    1
    2.0
    2.0
    114
    -c-a
    43
  • Specify lifting-over assemblies that change the tags
    5526
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    114
    -c-a
    43
  • Build support for lifting-over assemblies that change the tags
    7440
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • [Tyler] Implementation
    7079
    Lightning
    43
    Story
    6
    Closed
    5
    3.0
    3.0
    114
    -c-a
    43
  • [Sprite] Polyphen data addition to annotations
    4070
    Lightning
    43
    Story
    6
    Closed
    5
    114
    -c-a
    43
  • Package lightning specifically for users
    4995
    Lightning
    43
    Story
    6
    New
    1
    5.0
    5.0
    114
    -c-a
    43
  • Automatic Deployment Implementation
    4827
    Lightning
    43
    Story
    6
    New
    1
    5.0
    5.0
    114
    -c-a
    43
  • Test the effect of phasing imputation workflow
    13376
    Lightning
    43
    Story
    6
    In Progress
    2
    114
    -c-a
    43
  • Write phasing imputation workflow
    13216
    Lightning
    43
    Story
    6
    Resolved
    3
    114
    -c-a
    43
Product Backlog
  • Renaming variables to reflect use case
    14571
    Lightning
    43
    Bug
    1
    New
    1
    -c-a
    43
  • Parallelize CWL SGLF tile library creation
    14000
    Lightning
    43
    Story
    6
    In Progress
    2
    -c-a
    43
  • Imputation and phasing tiling data
    13639
    Lightning
    43
    Feature
    2
    New
    1
    -c-a
    43
  • Add step to cgf test to collect all chrom tests results
    13210
    Lightning
    43
    Feature
    2
    New
    1
    -c-a
    43
  • FastJ aggregation into SGLF takes too much memory
    12951
    Lightning
    43
    Bug
    1
    In Progress
    2
    -c-a
    43
  • pasta rotini-fastj does not handle tagset without ending newline
    12245
    Lightning
    43
    Bug
    1
    New
    1
    -c-a
    43
  • Covnert hg19 to FastJ and CGF
    11746
    Lightning
    43
    Story
    6
    New
    1
    3.0
    3.0
    -c-a
    43
  • Convert new SGLF to glf.2bitgz, glf.2bit.path and glf.2bitbz2
    11698
    Lightning
    43
    Story
    6
    New
    1
    3.0
    3.0
    -c-a
    43
  • Convert Harvard PGP exome data to CGF
    11675
    Lightning
    43
    Story
    6
    New
    1
    6.0
    6.0
    -c-a
    43
  • Documentation current speed of concordance and other stats
    10104
    Lightning
    43
    Story
    6
    New
    1
    2.0
    2.0
    -c-a
    43
sprint
 
no end
no start
  • 0
    -c-a
  • December 03, 2018 18:32:43.5285490283966064 +0000