Develop (!53) · Merge requests · BICF / Astrocyte / cellranger_count

Merged Develop

develop into master

Merged Gervaise Henry requested to merge develop into master 5 years ago

Jul 24, 2019
- Update CHANGELOG.md · 1019aefc
  Gervaise Henry authored 5 years ago
  
  1019aefc
Jul 23, 2019
- Merge branch '29-VersionCompatibility' into 'develop' · 692b7962
  Gervaise Henry authored 5 years ago
```
Resolve "Test for kitVersion=3 and version=2.1.1 and exit if true"

Closes #29

See merge request !52
```
  692b7962
- Final Version · 9ff49cb2
  Jeremy Mathews authored 5 years ago
  
  9ff49cb2
- New branch 29 · 45cbf237
  Jeremy Mathews authored 5 years ago
  
  45cbf237
- Merge branch '28-AddPytestCI' into 'develop' · 14599fcc
  Gervaise Henry authored 5 years ago
```
Resolve "Add pytest to CI"

Closes #28

See merge request !51
```
  14599fcc
- Merge branch '28-AddPytestCI' of... · 9eefea9d
  Jeremy Mathews authored 5 years ago
```
Merge branch '28-AddPytestCI' of git.biohpc.swmed.edu:BICF/Astrocyte/cellranger_count into 28-AddPytestCI
```
  9eefea9d
- update runtime settings · 8db1aed8
  Jeremy Mathews authored 5 years ago
  
  8db1aed8
- Update .gitlab-ci.yml · 27285ae6
  Gervaise Henry authored 5 years ago
  
  27285ae6
- final versions · e4ef9f0e
  Jeremy Mathews authored 5 years ago
  
  e4ef9f0e
- change runtimes · c5d8c6b2
  Jeremy Mathews authored 5 years ago
  
  c5d8c6b2
- new test · 2436e60f
  Jeremy Mathews authored 5 years ago
  
  2436e60f
- add new directories · e483e11a
  Jeremy Mathews authored 5 years ago
  
  e483e11a
- add detailed 3 · c1ab37d9
  Jeremy Mathews authored 5 years ago
  
  c1ab37d9
- Test simple 3 test with cellranger 3.0.2 · 4daaf239
  Gervaise Henry authored 5 years ago
  
  4daaf239
- Fix mkdir for 1k testdata · d0239152
  Gervaise Henry authored 5 years ago
  
  d0239152
- Run simple3 test (hv2s1) with 1k reads, and set simple1 test (h3s1) to auto chemistry · d72024dc
  Gervaise Henry authored 5 years ago
  
  d72024dc
- Revert "Test count211 for right cellranger module load" · b3b37b7e
  Gervaise Henry authored 5 years ago
```
This reverts commit 798c71d5
```
  b3b37b7e
- Test count211 for right cellranger module load · 798c71d5
  Gervaise Henry authored 5 years ago
  
  798c71d5
- revert to no astrocyte · 98101e80
  Jeremy Mathews authored 5 years ago
  
  98101e80
- astrocyte true in simple3 · 8c76242b
  Jeremy Mathews authored 5 years ago
  
  8c76242b
- make valid yml file · dc2bdad6
  Jeremy Mathews authored 5 years ago
  
  dc2bdad6
- add simple and detailed tests · d2b80f76
  Jeremy Mathews authored 5 years ago
  
  d2b80f76
Jul 22, 2019
- Restructure pytests · c0e59b31
  Jeremy Mathews authored 5 years ago
  
  c0e59b31
- Add CI updates · 62e0726d
  Jeremy Mathews authored 5 years ago
  
  62e0726d
Jul 10, 2019
- Update README.md · e4c36754
  Gervaise Henry authored 5 years ago
  
  e4c36754
- Update README.md · 603c8398
  Gervaise Henry authored 5 years ago
  
  603c8398
- Update CHANGELOG.md · e8ee7609
  Gervaise Henry authored 5 years ago
  
  e8ee7609
- Merge branch '27-CheckStyle' into 'develop' · 026b2a52
  Gervaise Henry authored 5 years ago
```
fixed style

Closes #27

See merge request !48
```
  026b2a52
- fixed style · 1fe100af
  Holly Ruess authored 5 years ago
  
  1fe100af
Jun 28, 2019
- Update CHANGELOG.md · 302083f1
  Gervaise Henry authored 5 years ago
  
  302083f1
- Merge branch '5-MultiQC' into 'develop' · ab0033d0
  Gervaise Henry authored 5 years ago
```
Resolve "Add MultiQC"

Closes #5

See merge request !47
```
  ab0033d0
- Slight formatting to match cellranger_mkfastq · fb55f7c1
  Gervaise Henry authored 5 years ago
  
  fb55f7c1
- Only output multiqc html and put in dir · 275a0a70
  Gervaise Henry authored 5 years ago
  
  275a0a70
- Format multiqc · 34036959
  Gervaise Henry authored 5 years ago
  
  34036959
- Change multiqc order and fic config param · 24271608
  Gervaise Henry authored 5 years ago
  
  24271608
- Repace mix for sample matrix summary · 274c185c
  Gervaise Henry authored 5 years ago
  
  274c185c
- Make seetings match mkfastq · 2d5e4560
  Gervaise Henry authored 5 years ago
  
  2d5e4560
Jun 27, 2019
- Add MultiQC to output. Add version and reference material. fix README · 8391da95
  Jeremy Mathews authored 5 years ago
  
  8391da95
May 24, 2019
- Update CHANGELOG.md · 87ca7c11
  Gervaise Henry authored 5 years ago
  
  87ca7c11
- Update astrocyte_pkg.yml · 3e4876a7
  Gervaise Henry authored 5 years ago
  
  3e4876a7
- Merge branch '26-ModuleLoad' into 'develop' · 92fdaee4
  Gervaise Henry authored 5 years ago
```
Resolve "Move module load into nextflow process"

Closes #26

See merge request !43
```
  92fdaee4
- Update CHANGELOG.md · 40a6540c
  Gervaise Henry authored 5 years ago
  
  40a6540c
- Error Check moved to Bash Script · d1bee614
  Jeremy Mathews authored 5 years ago
  
  d1bee614
May 23, 2019
- Folder and File Check issue #25 · 40481dcf
  Jeremy Mathews authored 5 years ago
  
  40481dcf
May 22, 2019
- Merge branch '26-ModuleLoad' into 'develop' · a7f754a7
  Gervaise Henry authored 5 years ago
```
Module Load moved to top of nextflow processes

Closes #26

See merge request !41
```
  a7f754a7
- Module Load moved to top of nextflow processes · 185d1ef0
  Jeremy Mathews authored 5 years ago
  
  185d1ef0
May 10, 2019
- Update astrocyte_pkg.yml · baadbf42
  Gervaise Henry authored 5 years ago
  
  baadbf42
May 03, 2019
- Merge branch '24-output.folders' into 'develop' · f4ca554b
  Gervaise Henry authored 6 years ago
```
Resolve "Organize output folders"

Closes #24

See merge request !40
```
  f4ca554b
- Put check design ouput in misc · 14ac1946
  Gervaise Henry authored 6 years ago
  
  14ac1946
- Add run name param · 991c35f4
  Gervaise Henry authored 6 years ago
  
  991c35f4
Apr 27, 2019
- Update .gitlab-ci.yml · 771a4f0b
  Gervaise Henry authored 6 years ago
  
  771a4f0b
- Update .gitlab-ci.yml · 8a82e474
  Gervaise Henry authored 6 years ago
  
  8a82e474
- Update .gitlab-ci.yml · 3952384b
  Gervaise Henry authored 6 years ago
  
  3952384b
- Merge branch '21-change.astrocyte.regex' into 'develop' · 01a3b1e3
  Gervaise Henry authored 6 years ago
```
Fix asrocyte regex for extension filtering

Closes #21

See merge request !39
```
  01a3b1e3
- Fix asrocyte regex for extension filtering · cb91b543
  Gervaise Henry authored 6 years ago
  
  cb91b543
- Merge branch '23-ci.force.mkdir.ln' into 'develop' · f94e17ad
  Gervaise Henry authored 6 years ago
```
Force mkdir and ln in CI

Closes #23

See merge request !38
```
  f94e17ad
- Merge branch '22-changelog' into 'develop' · 43c707ca
  Gervaise Henry authored 6 years ago
```
Resolve "Make changelog"

Closes #22

See merge request !37
```
  43c707ca
- Force mkdir and ln in CI · a70eaaf3
  Gervaise Henry authored 6 years ago
  
  a70eaaf3
- Merge branch '20-DOI' into 'develop' · 91df3161
  Gervaise Henry authored 6 years ago
```
Add DOI badge

Closes #20

See merge request !36
```
  91df3161
- Update README.md · 08efee32
  Gervaise Henry authored 6 years ago
  
  08efee32
- Update index.md · 4badc015
  Gervaise Henry authored 6 years ago
  
  4badc015
- Update CHANGELOG.md · a9c77ab6
  Gervaise Henry authored 6 years ago
  
  a9c77ab6
- Add changelog file · b25d6b32
  Gervaise Henry authored 6 years ago
  
  b25d6b32
Apr 26, 2019
- Add DOI badge · 72ce8d57
  Venkat Malladi authored 6 years ago
  
  72ce8d57
Mar 27, 2019
- Merge branch '18-change.process.selector' into 'develop' · d02c3e8b
  Gervaise Henry authored 6 years ago
```
Resolve "Change process selector"

Closes #18

See merge request !34
```
  d02c3e8b
- Remove redundant process name in process tag · ca3ea150
  Gervaise Henry authored 6 years ago
  
  ca3ea150
- Fix process selector in config · 2c45dc5e
  Gervaise Henry authored 6 years ago
  
  2c45dc5e
- Merge branch '19-rename.fastq.s' into 'develop' · 31d1da2c
  Gervaise Henry authored 6 years ago
```
Resolve "Change nextflow fastq rename to iterate sample not lane"

Closes #19

See merge request !33
```
  31d1da2c
- Rename fastqs by sample not lane · 382be8c7
  Gervaise Henry authored 6 years ago
  
  382be8c7

Develop

Merge request reports

Activity