Develop (!68) · Merge requests · GUDMAP_RBK / RNA-seq

Merged Gervaise Henry requested to merge develop into master 4 years ago

Feb 01, 2021

Merge branch '110-SE' into 'develop' · fca601e4

Venkat Malladi authored 4 years ago

Resolve "Change Single Read to Single End for submitted endness"

Closes #95, #100, #112, #111, #70, #115, #114, and #110

See merge request !67

fca601e4

Jan 29, 2021
- Correct reference var name · 9cccaef7
  Gervaise Henry authored 4 years ago
  
  9cccaef7
- Fix bool spike override in getRef · 3235c1c4
  Gervaise Henry authored 4 years ago
  
  3235c1c4
- Change spike override to true/false · 04dbe532
  Gervaise Henry authored 4 years ago
  
  04dbe532
- Update dag · 762f3ba7
  Gervaise Henry authored 4 years ago
  
  762f3ba7
- Fix getRef for spike · ced21083
  Gervaise Henry authored 4 years ago
  
  ced21083
Jan 28, 2021
- Move spike/stranded override to infer (like species), not submitter · 0bb07de4
  Gervaise Henry authored 4 years ago
  
  0bb07de4
- Fix spike override ci pytest · f36d728b
  Gervaise Henry authored 4 years ago
  
  f36d728b
- Convert blank nan submitted metadata to No value · 37a1345e
  Gervaise Henry authored 4 years ago
  
  37a1345e
- Update version to 2.0.0rc01 · 6961db25
  Gervaise Henry authored 4 years ago
  
  6961db25
- Add multiqc html to ci artifacts for override tests · 8859d7e9
  Gervaise Henry authored 4 years ago
  
  8859d7e9
- Try excaping tabs for metadata override for report · b1cdf286
  Gervaise Henry authored 4 years ago
  
  b1cdf286
- Update DAG · a7d4aa13
  Gervaise Henry authored 4 years ago
  
  a7d4aa13
- Fix metadata echo · 329dc950
  Gervaise Henry authored 4 years ago
  
  329dc950
- Fix spike override test · 63fbe5e4
  Gervaise Henry authored 4 years ago
  
  63fbe5e4
Jan 27, 2021
- Change replicates for metadata overrides · 2ddefb95
  Gervaise Henry authored 4 years ago
  
  2ddefb95
- Fix stranded override · 04c81525
  Gervaise Henry authored 4 years ago
  
  04c81525
- Update reps used for override metadata · 6e617062
  Gervaise Henry authored 4 years ago
  
  6e617062
- Fix aggrQC if brackets · 8a1299d4
  Gervaise Henry authored 4 years ago
  
  8a1299d4
- Fix params · 502328a7
  Gervaise Henry authored 4 years ago
  
  502328a7
- Make tracking upload option · df96927b
  Gervaise Henry authored 4 years ago
  
  df96927b
- Update pytest to utilize params · 1d912493
  Gervaise Henry authored 4 years ago
  
  1d912493
- Fix stranded variable · 09dd7af3
  Gervaise Henry authored 4 years ago
  
  09dd7af3
- Update pytests · a32879db
  Gervaise Henry authored 4 years ago
  
  a32879db
Jan 26, 2021
- Fix bracket · 14b8fc1d
  Gervaise Henry authored 4 years ago
  
  14b8fc1d
- Revert SE integration test and server for all integrations · 37bec34c
  Gervaise Henry authored 4 years ago
  
  37bec34c
- Change replicate for SE integration · 349cbde4
  Gervaise Henry authored 4 years ago
  
  349cbde4
- Fix echo line · 4f9bc352
  Gervaise Henry authored 4 years ago
  
  4f9bc352
- Remove extra quote · 6b085ad6
  Gervaise Henry authored 4 years ago
  
  6b085ad6
- Add new py tests for integration and override · ecd4e76f
  Gervaise Henry authored 4 years ago
  
  ecd4e76f
- Fix new force var names · 57529bc9
  Gervaise Henry authored 4 years ago
  
  57529bc9
- Remove unnecessary excape · a3d8f200
  Gervaise Henry authored 4 years ago
  
  a3d8f200
- Add missing excapes · e7024f45
  Gervaise Henry authored 4 years ago
  
  e7024f45
- Fix qutes to echo · 4d50fe8f
  Gervaise Henry authored 4 years ago
  
  4d50fe8f
- Add qutes to echo · c03c60c9
  Gervaise Henry authored 4 years ago
  
  c03c60c9
- Add force params for stranded and spike · 59cb654a
  Gervaise Henry authored 4 years ago
  
  59cb654a
- Double excape slash · 0511ac1a
  Gervaise Henry authored 4 years ago
  
  0511ac1a
- Excape bash vars · b390a5e5
  Gervaise Henry authored 4 years ago
  
  b390a5e5
- Update create test data with new metadata model · 42785f19
  Gervaise Henry authored 4 years ago
  
  42785f19
- Update create test data with new metadata model · b5569b5b
  Gervaise Henry authored 4 years ago
  
  b5569b5b
- URLify hatrac location for outputBag · b15b2201
  Gervaise Henry authored 4 years ago
  
  b15b2201
- Fix getRef use of new spike values · ddc9ef20
  Gervaise Henry authored 4 years ago
  
  ddc9ef20
Jan 25, 2021
- Update parseMetadata ci test · c2a7f9b0
  Gervaise Henry authored 4 years ago
  
  c2a7f9b0
- Temporarily change CI integration tests to use dev server (staging doesn't have model changes) · c4c258bf
  Gervaise Henry authored 4 years ago
  
  c4c258bf
- Change logic for uploadOutputBag · a503d1e2
  Gervaise Henry authored 4 years ago
  
  a503d1e2
- Merge data error pre-Execution run · 77410b76
  Gervaise Henry authored 4 years ago
  
  77410b76
- Add blank mRNA_QC on data fail · f4e88555
  Gervaise Henry authored 4 years ago
  
  f4e88555
- Remove unnecessary RID output parsing · 03f13a82
  Gervaise Henry authored 4 years ago
  
  03f13a82
- Convert strandedness from yes/no to t/f · a19f61d1
  Gervaise Henry authored 4 years ago
  
  a19f61d1
- Convert strandedness from yes/no to t/f · b9798355
  Gervaise Henry authored 4 years ago
  
  b9798355
- Update Has_Strand_Specific_Information to Strandedness · 3b3b7891
  Gervaise Henry authored 4 years ago
  
  3b3b7891
- Update Sequencing_Type to Experiment_Type · a5aedff5
  Gervaise Henry authored 4 years ago
  
  a5aedff5
- Allow Single Read for backwards compatibility · ca8d3a9c
  Gervaise Henry authored 4 years ago
  
  ca8d3a9c
Jan 20, 2021
- Fix Single Read in CI · 52c66590
  Gervaise Henry authored 4 years ago
  
  52c66590
- Update changelog · 5011fa37
  Gervaise Henry authored 4 years ago
  
  5011fa37
- Change Single Read to Single End · 797354e0
  Gervaise Henry authored 4 years ago
  
  797354e0

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