cellranger_count merge requests
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests
2019-03-11T15:46:34-05:00
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/18
Develop
2019-03-11T15:46:34-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Develop
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/17
Resolve "Add params from biohpc.config into main.nf"
2019-03-11T15:45:24-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add params from biohpc.config into main.nf"
Closes #13
Closes #13
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/16
Develop
2019-03-10T17:49:16-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Develop
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/15
Resolve "Make instructions"
2019-03-10T17:17:35-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Make instructions"
Closes #3
Closes #3
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/14
Resolve "Make param.genomeLocation have full path"
2019-03-10T17:00:54-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Make param.genomeLocation have full path"
Closes #12
Closes #12
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/12
Resolve "Add parameter for 10x kit version"
2019-03-05T18:47:08-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add parameter for 10x kit version"
Closes #11
Closes #11
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/11
Resolve "Create output directory option"
2019-03-05T17:13:25-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Create output directory option"
Closes #4
Closes #4
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/10
Resolve "Fix config file"
2019-03-04T23:49:01-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Fix config file"
Closes #7
Closes #7
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/9
Resolve "Remove reference genome full folder"
2019-03-04T23:47:23-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Remove reference genome full folder"
Closes #2
Closes #2
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/8
Resolve "Remove reference genome full folder"
2019-03-04T22:55:17-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Remove reference genome full folder"
Closes #2
Closes #2
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/7
Resolve "Add cellranger references version 3.0.0 as options"
2019-03-04T20:51:12-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add cellranger references version 3.0.0 as options"
Closes #9
Closes #9
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/5
Resolve "Add cellranger 3.0.2 as option"
2019-03-04T20:43:39-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add cellranger 3.0.2 as option"
Closes #8
Closes #8
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/4
Resolve "Add cellranger 3.0.2 as option"
2019-03-04T15:44:26-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add cellranger 3.0.2 as option"
Closes #8
Closes #8
Put on Astrocyte Production (1.0.0)
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/81
Add new lib options to biohpc config
2020-11-20T12:13:21-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Add new lib options to biohpc config
Closes #56
Closes #56
3.0.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/80
Resolve "Add 5GEXPE/SE as library options"
2020-11-20T11:36:36-06:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Add 5GEXPE/SE as library options"
Closes #56
Closes #56
3.0.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/79
Update CHANGELOG.md, workflow/main.nf, workflow/nextflow.config files
2020-08-15T11:34:25-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Update CHANGELOG.md, workflow/main.nf, workflow/nextflow.config files
2.2.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/78
Develop
2020-08-15T11:16:39-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Develop
2.2.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/76
Resolve "Generate Raw RDS file"
2020-08-14T14:01:39-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Resolve "Generate Raw RDS file"
Create raw Seurat object with cellranger_count output
Includes:
* cellranger filtered cells (cells without background)
* cellranger calculated dimensional reduction:
* PCA
* tSNE
* UMAP (if late enough cellranger version used)
* al...
Create raw Seurat object with cellranger_count output
Includes:
* cellranger filtered cells (cells without background)
* cellranger calculated dimensional reduction:
* PCA
* tSNE
* UMAP (if late enough cellranger version used)
* all cellranger calculated clustering
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
- [x] `LICENSE.md` is updated with new contributors
* [x] **Close issue**\
Closes #50
/cc @ghenry
2.2.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/75
Cellranger 4.0.0 ref 2020 a
2020-08-13T14:56:34-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Cellranger 4.0.0 ref 2020 a
2.2.0
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu
https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/74
Fix multi sample, local ulimit set, v2.1.1
2020-06-21T20:20:17-05:00
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Fix multi sample, local ulimit set, v2.1.1
v2.1.1
Gervaise Henry
gervaise.henry@utsouthwestern.edu
Gervaise Henry
gervaise.henry@utsouthwestern.edu