RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2021-05-06T23:43:50-05:00https://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/82Fix fetch fastq count2021-04-13T21:21:10-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix fetch fastq countv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/81Develop2021-04-12T23:11:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/76Develop2021-03-21T00:36:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/77Docs2021-03-20T21:50:30-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDocsv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/75Env.ci2021-03-20T09:15:06-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduEnv.ciMake environment tests for DNAnexus and AWS
## 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` ...Make environment tests for DNAnexus and AWS
## 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
- [ ] 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~~
* ~~[ ] **Close issue**\~~
Closes #
/cc @ghenry @venkat.malladiv2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/74Develop2021-03-18T23:06:21-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/72Update.containers2021-03-09T04:09:31-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate.containersUpdate tools to latest versions (containers)...
## 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 ...Update tools to latest versions (containers)...
## 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~~
- [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
- ~~[ ] `README.md` is updated~~
- ~~[ ] `LICENSE.md` is updated with new contributors~~
- [x] Docker images moved to production release and changed in pipeline
- [x] Docker images used in the CI unit tests match those used in pipeline
* ~~[ ] **Close issue**~~\
Closes #
/cc @ghenry @venkat.malladiv2.0.0Gervaise 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/68Develop2021-02-01T12:09:51-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/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/65Develop2021-01-20T18:50:17-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelopv2.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/64Resolve "samtools sort: couldn't allocate memory for bam_mem"2021-01-20T18:12:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduResolve "samtools sort: couldn't allocate memory for bam_mem"Fixes some newly discovered metadata errors.\
Has been tested with `--upload false`\
Testing overnight (with `--upload true --server dev
* W-RCGG: submitted stranded/spike = blank & have fastq's not matching convention
* 14-3R4R: submitt...Fixes some newly discovered metadata errors.\
Has been tested with `--upload false`\
Testing overnight (with `--upload true --server dev
* W-RCGG: submitted stranded/spike = blank & have fastq's not matching convention
* 14-3R4R: submitted stranded/spike = unspecified
* Q-Y5HT: fastq structure error (fastq+bam concatenation)
* W-RB84: no errors
## 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 #105
Closes #106
Closes #107
Closes #108
Closes #109
/cc @ghenry @venkat.malladiv2.0.0Venkat MalladiVenkat Malladi