BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-14T10:08:21-05:00https://git.biohpc.swmed.edu/BICF/onboarding/-/issues/19Git CI stall solution update2020-04-14T10:08:21-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduGit CI stall solution updateAdd to solution for Git CI stall:\
`nextflow -q run workflow/main.nf`
pro/con:\
`-bg` **can** see nextflow output in gitlab CI terminal but **cannot** use any command after in CI (eg pytest)\
`q` **cannot** see nextflow output in gitlab...Add to solution for Git CI stall:\
`nextflow -q run workflow/main.nf`
pro/con:\
`-bg` **can** see nextflow output in gitlab CI terminal but **cannot** use any command after in CI (eg pytest)\
`q` **cannot** see nextflow output in gitlab CI terminal but **can** use any command after in CI (eg pytest)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/43Remove unnecessary files from output2020-04-14T10:01:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove unnecessary files from outputv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/42Update params to current standards2020-04-15T10:04:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate params to current standardsnon-imputable params do not need to have "param." prefixnon-imputable params do not need to have "param." prefixv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/41Containerize2020-04-15T21:18:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduContainerizev2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/38Add license2020-05-07T15:53:13-05:00Venkat MalladiAdd licenseVersion 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/18Update Astrocyte configuration2020-06-01T13:28:24-05:00Venkat MalladiUpdate Astrocyte configuration* [x] email should be `bicf@utsouthwestern.edu`
* [x] Author list: Include Jermey
* [ ] Have Paniz add logo like other pipelines for BICF: https://astrocyte.biohpc.swmed.edu/workflow/browse/
* [x] Update index.html to not reference m...* [x] email should be `bicf@utsouthwestern.edu`
* [x] Author list: Include Jermey
* [ ] Have Paniz add logo like other pipelines for BICF: https://astrocyte.biohpc.swmed.edu/workflow/browse/
* [x] Update index.html to not reference metagenomics pipeline `git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/metagenome_analysis.git`
* [ ] Add release notes
* [x] Fix Jon's email link to his actual email
* [ ] Add in Doc and index.html for display on astrocyte: https://astrocyte.biohpc.swmed.edu/static/docs/workflow_developer/overview.html#docs-user-focused-documentation
* [ ] Add build, nextflow and astrocyte badgesJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/17Need Zenodo registration2020-04-20T10:57:43-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduNeed Zenodo registrationI'm trying to referenceI'm trying to referenceVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/16BUG: Cannot handle multiple runs2020-06-01T13:28:23-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduBUG: Cannot handle multiple runs# Pipeline cannot handle experiments (samples) with multiple runs... for example:
| sample_id | sra_number |
| ------ | ------ |
| Sample1 | SRX172938 |
fails because SRX172938 has 4 runs:
| Run | # of Spots | # of Bases | Size ...# Pipeline cannot handle experiments (samples) with multiple runs... for example:
| sample_id | sra_number |
| ------ | ------ |
| Sample1 | SRX172938 |
fails because SRX172938 has 4 runs:
| Run | # of Spots | # of Bases | Size | Published |
|-----------|------------|------------|---------|------------|
| SRR531404 | 5,261,058 | 189.4M | 93.6Mb | 2012-09-11 |
| SRR531405 | 6,870,169 | 247.3M | 204.4Mb | 2012-09-11 |
| SRR531406 | 7,941,818 | 285.9M | 236.8Mb | 2012-09-11 |
| SRR531407 | 31,599,710 | 1G | 605.1Mb | 2012-09-11 |
## Advice
one or a combination of the following:
* make a note in instructions pointing out that the pipeline fails with samples with multiple sequencing runs and that users need to split those SRX's into separate SRR downloads
* don't accept any SRX's
* in check design, make sure that samples don't contain multiple runs and error if it does
* in check design, make sure that samples don't contain multiple runs and automatically split them
* if split then, consider concatenating SRR's after if submitted as 1 SRX
@venkat.malladi @s181706 @s189701 @s181385Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/18Software Development2020-04-08T09:17:45-05:00Venkat MalladiSoftware DevelopmentVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/37Fix runners and sigbus error2020-05-08T10:01:55-05:00Venkat MalladiFix runners and sigbus errorVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/82Disk quota exceeded2020-04-13T13:50:12-05:00Venkat MalladiDisk quota exceededVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/17CI and Nextflow configuration2020-04-13T15:31:27-05:00Venkat MalladiCI and Nextflow configurationVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/81Config Lock git2020-04-16T22:21:45-05:00Venkat MalladiConfig Lock gitcan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issuecan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issueVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/80Gitlab CI overridding concurrent pipelines2020-04-16T03:01:51-05:00Venkat MalladiGitlab CI overridding concurrent pipelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/79Fix sigbus error2020-04-16T03:01:51-05:00Venkat MalladiFix sigbus errorFixing sigbus error for nextflowFixing sigbus error for nextflowVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/15Convert SOLID sequencing to basecall2020-06-01T13:28:23-05:00Venkat MalladiConvert SOLID sequencing to basecallSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/78Paired-end Diffbind peaks gives different answer2020-04-20T09:01:39-05:00Venkat MalladiPaired-end Diffbind peaks gives different answerJob [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:Job [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/16Authorship guidelines2020-03-31T12:02:51-05:00Venkat MalladiAuthorship guidelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/39Add base mask2020-06-20T20:34:36-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd base mask`-use-bases-mask=Y28n*,I8n*,n*,Y*``-use-bases-mask=Y28n*,I8n*,n*,Y*`v2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/77Update to Astrocyte 0.2.02020-03-21T11:16:24-05:00Venkat MalladiUpdate to Astrocyte 0.2.0astrocyte/0.2.0astrocyte/0.2.01.1.0Venkat MalladiVenkat Malladi