RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2021-07-31T10:35:39-05:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/99Resolve "Fix endness force"2021-07-31T10:35:39-05:00Venkat MalladiResolve "Fix endness force"When endess force overwrite fastq error.
## 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 `do...When endess force overwrite fastq error.
## 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~~
- [ ] ~~`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 #135
/cc @ghenry @venkat.malladiv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/97If ends force then override fastq read error2021-07-30T14:29:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduIf ends force then override fastq read errorFix Endness force
## 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 Endness force
## 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 #135
/cc @ghenry @venkat.malladiv2.0.1Venkat MalladiVenkat Malladihttps://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/94Resolve "Move seqwho reference"2021-07-26T16:44:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Move seqwho reference"- Move seqwho reference to developer maintained location
- Make seqwho ref location an overridable location
- Change NF Tower to BICF... BICF user access ID + BICF pipelines workspace
- Disable NF Tower
- Remove all AWS tracking
## PR c...- Move seqwho reference to developer maintained location
- Make seqwho ref location an overridable location
- Change NF Tower to BICF... BICF user access ID + BICF pipelines workspace
- Disable NF Tower
- Remove all AWS tracking
## 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 #127
/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/90Reimplimented symbolic link of bdbag cookie.2021-07-19T10:48:49-05:00Venkat MalladiReimplimented symbolic link of bdbag cookie.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)
- ~~...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)
- ~~[ ] 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
- [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 #132
/cc @ghenry @venkat.malladiv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/89Changed the spelling of inferred.2021-07-16T16:36:42-05:00Venkat MalladiChanged the spelling of inferred.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)
- ~~...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)
- ~~[ ] 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 #125
/cc @ghenry @venkat.malladiv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/88Update rna-seq.nf2021-07-15T15:56:09-05:00Jonathan GesellUpdate rna-seq.nfPlease fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
Fixed the issue where the script would error out due to not finding precise string. Repl...Please fill in the appropriate checklist below (delete those which are not relevant).
These are the most common things requested on pull requests.
Fixed the issue where the script would error out due to not finding precise string. Replaced the string as requested in issue 129.
## 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 #129
/cc @ghenry @venkat.malladiv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/67Resolve "Change Single Read to Single End for submitted endness"2021-02-01T12:06:09-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Change Single Read to Single End for submitted endness"Cumulative branch for v2.0.0
## 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~~
...Cumulative branch for v2.0.0
## 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~~
- [x] 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 #110
Closes #114
Closes #115
Closes #70
Closes #111
Closes #112
Closes #100
Closes #95
/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 Malladi