RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2020-03-15T14:35:44-05:00https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/23Resolve "process_RSeQC"2020-03-15T14:35:44-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "process_RSeQC"Infer's metadata:
* Predicts strandedness
* Calculates insert size if PE
* Calculates TIN
Also ensures outputs of all QC stats from other processes
## PR checklist
- [x] This comment contains a description of changes (with ...Infer's metadata:
* Predicts strandedness
* Calculates insert size if PE
* Calculates TIN
Also ensures outputs of all QC stats from other processes
## 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] Replace dag.png with the most recent CI pipleine integrated_pe artifact
* [x] **Close issue**\
Closes #35
/cc @ghenry @venkat.malladiv0.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/21Resolve "Update design docs"2020-02-18T07:52:43-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Update design docs"**This branch merge updates design docs**
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] Documentation in `docs` is updated
- [x] Replace dag.png with the most recent CI pipleine integrated_p...**This branch merge updates design docs**
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] Documentation in `docs` is updated
- [x] Replace dag.png with the most recent CI pipleine integrated_pe artifact
- [x] `README.md` is updated
* [x] **Close issue**\
Closes #39
/cc @ghenry @venkat.malladiv0.0.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/100Develop2021-07-31T11:22:40-05:00Venkat MalladiDevelopVenkat MalladiVenkat Malladihttps://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/98Develop2021-07-30T14:29:59-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.1Gervaise 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/96Update changelog2021-07-27T12:00:48-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate changelogv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/95Update rna-seq.nf2021-07-27T11:58:33-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate rna-seq.nfChanged the requested line in the scripts section of rna-seq.nfChanged the requested line in the scripts section of rna-seq.nfv2.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/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/91Resolve "Change the CI unit test RIDs"2021-07-22T08:55:14-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "Change the CI unit test RIDs"Update RIDs used for CI unit tests... and move them to CI variables, so future modifications does not require pipeline patch
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bu...Update RIDs used for CI unit tests... and move them to CI variables, so future modifications does not require pipeline patch
## 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 #133
/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/87Develop2021-05-06T23:43:50-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/86Fix fail pre ex run dependency on infferd meta2021-04-22T17:38:13-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix fail pre ex run dependency on infferd metav2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/85Fix seqwho errors2021-04-20T21:17:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix seqwho errorsv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/84Fix failPreExecutionRun error collection2021-04-13T22:15:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix failPreExecutionRun error collectionv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/83Fix error output2021-04-13T22:04:42-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix error outputv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu