BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-12-29T17:33:26-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/1Install methylation2020-12-29T17:33:26-06:00Venkat MalladiInstall methylation1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/39Tests for astrocyte2020-06-18T08:32:27-05:00Venkat MalladiTests for astrocyteVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/21Add badges2020-06-17T10:24:58-05:00Venkat MalladiAdd badgesAdd testing badge for master
`[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/commits/master)`
Add badge for doi:
[![...Add testing badge for master
`[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/commits/master)`
Add badge for doi:
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3739788.svg)](https://doi.org/10.5281/zenodo.3739788)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/20BUG: SRX not working2020-05-10T13:56:48-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduBUG: SRX not workingon branch 16-multiple_srrs and I put in a bunch of SRX's...
checkDesign errors out saying:
> Error: Invalid SRA number format found:
Terminating.
Offending designFile attatched[16-DMR8.tsv](/uploads/3730897508de1c3b021a5246aff0b4cc/...on branch 16-multiple_srrs and I put in a bunch of SRX's...
checkDesign errors out saying:
> Error: Invalid SRA number format found:
Terminating.
Offending designFile attatched[16-DMR8.tsv](/uploads/3730897508de1c3b021a5246aff0b4cc/16-DMR8.tsv)https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/45Multiqc failure2020-04-26T18:34:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMultiqc failure# Summary
MultiQC step fail when submitted CLI for some users
# Steps to reproduce
`nextflow run` by user with matplotlib > 3.1.2 installed
# Observed bug behavior
python error
# Expected behavior
pass
# Relevant logs and/or screensh...# Summary
MultiQC step fail when submitted CLI for some users
# Steps to reproduce
`nextflow run` by user with matplotlib > 3.1.2 installed
# Observed bug behavior
python error
# Expected behavior
pass
# Relevant logs and/or screenshots
```
pkg_resources.VersionConflict: (matplotlib 3.2.1 (/home2/ghenry/.local/lib/python3.6/site-packages), Requirement.parse('matplotlib<3.1.2,>=2.1.1'))
```
# Potential fixes
Remove depreciated module command in multiqc process (pipeline uses docker container now and does not require modules)
/cc @ghenryhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/44Thread error on BioHPC2020-04-20T18:41:13-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduThread error on BioHPC# Summary
#40 not fixed for all cellranger processes
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry# Summary
#40 not fixed for all cellranger processes
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenryv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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 Malladi