RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2021-07-26T20:37:06-05:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/93Add seqtype override2021-07-26T20:37:06-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd seqtype overrideAdd override for seqtype
## 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!~~
- [x] Documentation in `docs` is updated
- ~...Add override for seqtype
## 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!~~
- [x] Documentation in `docs` is updated
- ~~[ ] Replace dag.png with the most recent CI pipeline integrated_pe artifact~~
- ~~[ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- ~~[ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
- ~~[ ] `LICENSE.md` is updated with new contributors~~
- ~~[ ] Docker images moved to production release and changed in pipeline~~
- ~~[ ] Docker images used in the CI unit tests match those used in pipeline~~
* [x] **Close issue**\
Closes #131
/cc @ghenry @venkat.malladiv2.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/92Resolve "Server changing... need to change .insert calls"2021-07-22T18:58:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Server changing... need to change .insert calls"Modify insert calls with deriva.core to not use the default columns RCB and RMB as forthcoming server update will remove access.
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed ...Modify insert calls with deriva.core to not use the default columns RCB and RMB as forthcoming server update will remove access.
## 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~~
- ~~[ ] Replace dag.png with the most recent CI pipeline integrated_pe artifact~~
- ~~[ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- ~~[ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- [x] `CHANGELOG.md` is updated
- ~~[ ] `README.md` is updated~~
- ~~[ ] `LICENSE.md` is updated with new contributors~~
- ~~[ ] Docker images moved to production release and changed in pipeline~~
- ~~[ ] Docker images used in the CI unit tests match those used in pipeline~~
* [x] **Close issue**\
Closes #134
/cc @ghenry @venkat.malladiv2.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/69Fix2021-02-07T21:59:37-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduFixFix error detail 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~~
- ~...Fix error detail 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~~
- ~~[ ] Replace dag.png with the most recent CI pipeline integrated_pe artifact~~
- ~~[ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- ~~[ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact~~
- [x] `CHANGELOG.md` is updated
- ~~[ ] `README.md` is updated~~
- ~~[ ] `LICENSE.md` is updated with new contributors~~
- ~~[ ] Docker images moved to production release and changed in pipeline~~
- ~~[ ] Docker images used in the CI unit tests match those used in pipeline~~
* [x] **Close issue**\
Closes #118
/cc @ghenry @venkat.malladiv2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/60Resolve "failPreExecution not running on fastq error"2021-01-14T21:33:49-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "failPreExecution not running on fastq error"BUG FIX #101 and related issues
## 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
...BUG FIX #101 and related issues
## 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] Replace dag.png with the most recent CI pipeline integrated_pe artifact
- [x] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
- [x] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
- ~~[ ] `LICENSE.md` is updated with new contributors~~
- ~~[ ] Docker images moved to production release and changed in pipeline~~
- ~~[ ] Docker images used in the CI unit tests match those used in pipeline~~
* [x] **Close issue**\
Closes #101
Closes #103
Closes #96
Closes #97
Closes #102
/cc @ghenry @venkat.malladiv1.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/25Fix infer logic2020-03-24T10:01:55-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix infer logicCloses #44Closes #44v0.0.1Jonathan GesellJonathan Gesell