RNA-seq merge requestshttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests2021-01-20T18:12:45-06:00https://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 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/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)
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- [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/20Revert "Remove min nextflow version for 0.31.0 test"2020-02-14T15:20:14-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduRevert "Remove min nextflow version for 0.31.0 test"This reverts commit a92284c5639a0de705019cbec2cf6872e671ded7This reverts commit a92284c5639a0de705019cbec2cf6872e671ded7Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/71Seqwho2021-03-05T16:00:50-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduSeqwhoUtilize SeqWho for seq type and species inference
## PR checklist
- [x] This comment contains a description of changes (with reason)
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- [x] Documentation in `...Utilize SeqWho for seq type and species inference
## 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~~
- [x] 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 #122 Closes #49
/cc @ghenry @venkat.malladiVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/47Test failure.2020-11-10T15:24:56-06:00Venkat MalladiTest failure.Please fill in the appropriate checklist below (delete those which are not relevant).
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## PR checklist
- [x] 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
- [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
- [x] Replace dag.png with the most recent CI pipleine integrated_pe 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 #63
/cc @ghenry @venkat.malladi1.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/29Track.pipeline2020-04-25T17:40:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduTrack.pipelinePlease fill in the appropriate checklist below (delete those which are not relevant).
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## PR checklist
- [ ] This comment contains a description of changes (with reason)
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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!
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- [ ] `CHANGELOG.md` is updated
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* [ ] **Close issue**\
Closes #
/cc @ghenry
# Add pipeline tracking toolv0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/46Update consistency checks to be fully in python.2020-11-11T09:49:34-06:00Venkat MalladiUpdate consistency checks to be fully in python.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
- [x] This comment contains a description of changes (with reason)
- [x...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
- [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 pipleine integrated_pe 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 #60
/cc @ghenry @venkat.malladiFUTURE VersionGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/73Update.containers2021-03-12T12:37:27-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate.containersUpdate seqwho to v1.0.0
## 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~~
...Update seqwho to v1.0.0
## 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~~
- [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
- ~~[ ] `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.malladiGervaise 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!~~
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## PR checklist
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- ~~[ ] If you've fixed a bug or added code that should be tested, add tests!~~
- ~~[ ] Documentation in `docs` is updated~~
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- [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/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).
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## PR checklist
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## PR checklist
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* [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/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/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).
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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).
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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~~
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* [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/37v0.0.12020-08-11T17:34:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduv0.0.1Make official beta version v0.0.1Make official beta version v0.0.1v0.0.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/merge_requests/39v0.0.22020-08-15T16:02:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduv0.0.2Make official beta version v0.0.2Make official beta version v0.0.2v0.0.2Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu