Develop (!11) · Merge requests · GUDMAP_RBK / RNA-seq

Merged Develop

develop into 2-process_createManifest

Merged Gervaise Henry requested to merge develop into 2-process_createManifest 5 years ago

Jan 15, 2020
- Combine trimData CI se/pe into 1 unit test · 947e7543
  Gervaise Henry authored 5 years ago
  
  947e7543
- Merge branch '19-ci.integration.test' into 'develop' · 4cdee6d3
  Gervaise Henry authored 5 years ago
```
Resolve "Add integration CI test"

Closes #19

See merge request !10
```
  4cdee6d3
- Add https_proxy in getBag process · 4227759d
  Gervaise Henry authored 5 years ago
  
  4227759d
- Try removing proxy settings for biohpc nf config · 33f96a38
  Gervaise Henry authored 5 years ago
  
  33f96a38
- Add singularity and proxy settings to biohpc nf config · 279a541b
  Gervaise Henry authored 5 years ago
  
  279a541b
- Module load nextflow · 103fb9db
  Gervaise Henry authored 5 years ago
  
  103fb9db
- Add initial integration CI test · 07605c0d
  Gervaise Henry authored 5 years ago
  
  07605c0d
Jan 14, 2020
- Update README.md · c434dbd9
  Gervaise Henry authored 5 years ago
  
  c434dbd9
- Update gudmapfilexfer images to 1.3 in configs · 805ad15f
  Gervaise Henry authored 5 years ago
  
  805ad15f
- Merge branch '18-nextflow.configs' into 'develop' · 3cf5b891
  Gervaise Henry authored 5 years ago
```
Update nextflow configs to include aws

Closes #18

See merge request !9
```
  3cf5b891
- Update nextflow configs to include aws · 92951915
  Gervaise Henry authored 5 years ago
  
  92951915
- Fix getData pytest · 05a8f290
  Gervaise Henry authored 5 years ago
  
  05a8f290
- Add pytest for trim · c7ea5cba
  Gervaise Henry authored 5 years ago
  
  c7ea5cba
- Add pytest for getData · 18667028
  Gervaise Henry authored 5 years ago
  
  18667028
- Add pytest for getBag · 9e1a4c88
  Gervaise Henry authored 5 years ago
  
  9e1a4c88
- Add pytest for getBag · ba4f8944
  Gervaise Henry authored 5 years ago
  
  ba4f8944
- Add pytest for getBag · 42517ba5
  Gervaise Henry authored 5 years ago
  
  42517ba5
- Add pytest for getBag · 60fc625d
  Gervaise Henry authored 5 years ago
  
  60fc625d
- Add pytest for getBag · f4a7a9bd
  Gervaise Henry authored 5 years ago
  
  f4a7a9bd
- Update .gitlab-ci.yml · beae6362
  Gervaise Henry authored 5 years ago
  
  beae6362
- Update .gitlab-ci.yml · b4b42928
  Gervaise Henry authored 5 years ago
  
  b4b42928
- Update .gitlab-ci.yml · 2347e535
  Gervaise Henry authored 5 years ago
  
  2347e535
- Update .gitlab-ci.yml · 5771fcc1
  Gervaise Henry authored 5 years ago
  
  5771fcc1
- Update .gitlab-ci.yml · 17f187dc
  Gervaise Henry authored 5 years ago
  
  17f187dc
- Update .gitlab-ci.yml · 917a5f7f
  Gervaise Henry authored 5 years ago
  
  917a5f7f
- Merge branch '15-auto.bagit.download' into 'develop' · 69e5a3fa
  Gervaise Henry authored 5 years ago
```
Resolve "Add automated download of bagit through deriva"

Closes #15

See merge request !8
```
  69e5a3fa
- Fix biohpc config · a6c1385b
  Gervaise Henry authored 5 years ago
  
  a6c1385b
- Merge branch '16-trim.ci' into 'develop' · bb9b33d6
  Gervaise Henry authored 5 years ago
```
Resolve "Add CI for Trim"

Closes #16

See merge request !7
```
  bb9b33d6
- Fix indent · fb588535
  Gervaise Henry authored 5 years ago
  
  fb588535
- Add CI for trimData · 4882cf04
  Gervaise Henry authored 5 years ago
  
  4882cf04
- Add CI for getData · 5585f4ad
  Gervaise Henry authored 5 years ago
  
  5585f4ad
- Add CI for getBag · eb655d33
  Gervaise Henry authored 5 years ago
  
  eb655d33
- Add metadata outputs · 7fa5e438
  Gervaise Henry authored 5 years ago
  
  7fa5e438
- Rename fetched fastqs and fix se/pe · bbcfbd9f
  Gervaise Henry authored 5 years ago
  
  bbcfbd9f
Jan 13, 2020
- Cleanup .nf · d6cee4a5
  Gervaise Henry authored 5 years ago
  
  d6cee4a5
- Add getData deriva-download of bagit · e552d2e6
  Gervaise Henry authored 5 years ago
  
  e552d2e6
- Get deriva download of bagit started · cbba6901
  Gervaise Henry authored 5 years ago
  
  cbba6901
Dec 11, 2019
- Merge branch 'develop' into '15-auto.bagit.download' · 20daf0f9
  Gervaise Henry authored 5 years ago
```
Develop

See merge request !6
```
  20daf0f9
Dec 09, 2019
- Upgrade docker images (gudmaprbkfilexfer and trimgalore) to 1.1 · 0147ece8
  Gervaise Henry authored 5 years ago
  
  0147ece8
Dec 03, 2019
- Merge branch '14-UnitTest' into 'develop' · 9532b01f
  Gervaise Henry authored 5 years ago
```
Resolve "Add Unit Tests for splitData and getData processes"

Closes #14

See merge request !5
```
  9532b01f
- CHANGELOG · 154cdbdd
  Jeremy Mathews authored 5 years ago
  
  154cdbdd
- Fix path in validate statement · 218210f0
  Jeremy Mathews authored 5 years ago
  
  218210f0
- Strip CI to base · 23e761b2
  Jeremy Mathews authored 5 years ago
  
  23e761b2
Nov 25, 2019
- double brackets? · 0e1a3778
  Jeremy Mathews authored 5 years ago
  
  0e1a3778
- double quote? · fac6cc37
  Jeremy Mathews authored 5 years ago
  
  fac6cc37
- Add If stattements to check materialize of bdbag · dc2d6631
  Jeremy Mathews authored 5 years ago
  
  dc2d6631
Nov 20, 2019
- Update gitignore · f343641f
  Gervaise Henry authored 5 years ago
  
  f343641f
Nov 15, 2019
- test failure · daa84862
  Jeremy Mathews authored 5 years ago
  
  daa84862
- fix if statement · e5a88040
  Jeremy Mathews authored 5 years ago
  
  e5a88040
- Chnage assert to If statement · 5f0eda75
  Jeremy Mathews authored 5 years ago
  
  5f0eda75
- Add checksum assertion · b4cc77c9
  Jeremy Mathews authored 5 years ago
  
  b4cc77c9
- Add md5sum check · 9cea75ce
  Jeremy Mathews authored 5 years ago
  
  9cea75ce
- Initial CI · f3704ed3
  Jeremy Mathews authored 5 years ago
  
  f3704ed3

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