RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2020-01-30T15:49:26-06:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/16Resolve "process_getRef"2020-01-30T15:49:26-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "process_getRef"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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] **Close issue**\
Closes #29
/cc @ghenry @venkat.malladiv0.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/15Resolve "process_align"2020-01-28T22:10:42-06:00Jonathan GesellResolve "process_align"Alignment step using HiSat2
## 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!
- [ ] `README.md` is updated
* [ ]...Alignment step using HiSat2
## 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!
- [ ] `README.md` is updated
* [ ] **Close issue**\
Closes #4
Addresses alignData: add samtools to convert sam to bam and sort from #21
/cc @ghenry @venkat.malladi
/assign @ghenryv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/14Resolve "process_createManifest"2020-01-21T10:48:56-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "process_createManifest"Parses RBK/GUDMAP metadata to be used in further process, example is trim step.
## 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, a...Parses RBK/GUDMAP metadata to be used in further process, example is trim step.
## 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] **Close issue**\
Closes #2
/cc @ghenry @venkat.malladiv0.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/13Develop2020-01-18T23:20:19-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/12Resolve "Make scripts input files for processes"2020-01-18T17:27:01-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Make scripts input files for processes"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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 #20
Addresses some issues in CodeReview #21
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/11Develop2020-01-17T10:04:27-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/10Resolve "Add integration CI test"2020-01-15T11:44:29-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Add integration CI test"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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
* [x] **Close issue**\
Closes #19
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/9Update nextflow configs to include aws2020-01-14T16:25:36-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate nextflow configs to include awsPlease fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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
* [x] **Close issue**\
Closes #18
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/8Resolve "Add automated download of bagit through deriva"2020-01-14T12:09:32-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Add automated download of bagit through deriva"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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 #15
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/7Resolve "Add CI for Trim"2020-01-14T11:58:03-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Add CI for Trim"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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 #16
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/6Develop2019-12-11T09:48:25-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopUpdate stale feature branchUpdate stale feature branchGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/5Resolve "Add Unit Tests for splitData and getData processes"2019-12-03T11:53:46-06:00Jeremy MathewsResolve "Add Unit Tests for splitData and getData processes"Add initial CI for validating materialization of bag and testing docker abilities.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] `CHANGELOG.md` is updated
* [x] **Close issue**\
Closes #14
...Add initial CI for validating materialization of bag and testing docker abilities.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] `CHANGELOG.md` is updated
* [x] **Close issue**\
Closes #14
/cc @ghenry @venkat.malladiv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/4Develop2019-11-15T09:56:37-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopPlease fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #v0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/3Added trimming step using trimGalore and logging.2019-11-14T09:46:53-06:00Jonathan GesellAdded trimming step using trimGalore and logging.Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## 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
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
* [ ] **Close issue**\
Closes #3
/cc @ghenry @venkat.malladi
/assign @ghenryv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/2Resolve "process_getData"2019-11-04T12:19:54-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "process_getData"Closes #1
**Basic function of splitData and getData processes complete**Closes #1
**Basic function of splitData and getData processes complete**v0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/1Resolve "process_getData"2019-11-04T12:21:06-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "process_getData"v0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu