cellranger_count merge requestshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests2020-11-20T12:13:21-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/81Add new lib options to biohpc config2020-11-20T12:13:21-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd new lib options to biohpc configCloses #56Closes #563.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/80Resolve "Add 5GEXPE/SE as library options"2020-11-20T11:36:36-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Add 5GEXPE/SE as library options"Closes #56Closes #563.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/79Update CHANGELOG.md, workflow/main.nf, workflow/nextflow.config files2020-08-15T11:34:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate CHANGELOG.md, workflow/main.nf, workflow/nextflow.config files2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/78Develop2020-08-15T11:16:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelop2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/76Resolve "Generate Raw RDS file"2020-08-14T14:01:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "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 @ghenry2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/75Cellranger 4.0.0 ref 2020 a2020-08-13T14:56:34-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCellranger 4.0.0 ref 2020 a2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/74Fix multi sample, local ulimit set, v2.1.12020-06-21T20:20:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix multi sample, local ulimit set, v2.1.1v2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/73Develop2020-06-21T15:50:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/72Update configs folder name2020-06-21T14:31:52-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate configs folder name
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated...
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/71De containerize2020-06-21T14:22:38-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDe containerizeDe-containerize
## 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!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG...De-containerize
## 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!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/70Develop2020-05-25T13:28:10-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/69Remove multiqc module2020-04-26T18:34:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove multiqc module# Fixes multiqc CLI bug
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [x] `C...# Fixes multiqc CLI bug
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [x] **Close issue**\
Closes #45
/cc @ghenryGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/68Track.pipeline2020-04-25T16:32:31-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduTrack.pipelinePlease fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [ ...Please fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #
/cc @ghenry
# Add pipeline tracking toolGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/67Develop2020-04-20T18:54:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopPlease fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [x...Please fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [ ] 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!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/66Add ulimit -u to all cellranger processes2020-04-20T18:41:13-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ulimit -u to all cellranger processesPlease fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [x...Please fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [ ] 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!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [x] **Close issue**\
Closes #44
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/65Drop indev in version, finish adding aws details2020-04-16T09:46:46-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDrop indev in version, finish adding aws detailsGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/64Master2020-04-16T09:34:38-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMasterGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/63Develop2020-04-15T21:36:26-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopPlease fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x...Please fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
## 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
- [ ] `LICENSE.md` is updated with new contributors
* [x] **Close issue**\
Closes %"v2.0.0"
/cc @ghenryGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/62Resolve "Containerize"2020-04-15T21:18:38-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Containerize"Closes #41Closes #41v2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/merge_requests/61Resolve "Update params to current standards"2020-04-15T10:04:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Update params to current standards"Closes #42Closes #42v2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu