BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-08-15T11:19:37-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/51Version Zenodo2020-08-15T11:19:37-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduVersion ZenodoAdd Jon to author list
Keep pending until finishedAdd Jon to author list
Keep pending until finished2.2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/88create down-sampled test data2020-08-07T10:17:20-05:00Spencer Barnescreate down-sampled test dataCreate down-sampled fastq's for quick tests when applying bug fixes.Create down-sampled fastq's for quick tests when applying bug fixes.Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/50Generate Raw RDS file2020-08-14T14:01:39-05:00Venkat MalladiGenerate Raw RDS fileProvide Raw RDS file per sample (Seurat object)Provide Raw RDS file per sample (Seurat object)2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/43map reads fails to make bam files for long reads2020-07-29T07:44:38-05:00Venkat Malladimap reads fails to make bam files for long readshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam fileshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam filesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/21Update outside collaboration fee structure2020-07-14T12:12:11-05:00Venkat MalladiUpdate outside collaboration fee structureVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/29Gender to sex2020-07-01T20:02:32-05:00Venkat MalladiGender to sexVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/20Pipeline maintaince documentation2021-04-06T08:15:08-05:00Venkat MalladiPipeline maintaince documentationhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/25update test for astrocyte 0.3.12020-06-26T15:38:59-05:00Venkat Malladiupdate test for astrocyte 0.3.1Add test for astrocyte
update Readme to have astrocyte badgeAdd test for astrocyte
update Readme to have astrocyte badgehttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/48Update multiqc version/references report2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/40Update multiqc version/references report2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Pendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/47Add Jon to author list2020-08-14T15:13:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd Jon to author list* [x] License
* [ ] Zenodo* [x] License
* [ ] Zenodo2.2.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/84Track chip-seq usage2020-07-01T14:32:45-05:00Venkat MalladiTrack chip-seq usage```
/*
* trackStart: track start of pipeline
*/
process trackStart {
script:
"""
hostname
ulimit -a
export https_proxy=\${http_proxy}
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow....```
/*
* trackStart: track start of pipeline
*/
process trackStart {
script:
"""
hostname
ulimit -a
export https_proxy=\${http_proxy}
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "atacseq_analysis", \
"start": "${workflow.start}", \
"astrocyte": ${params.astrocyte}, \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", \
"pipelineVersion": "2.0.0", \
"ci": ${params.ci}, \
"dev": ${params.dev}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
```Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/40Astrocyte fixes2020-06-21T05:07:11-05:00Venkat MalladiAstrocyte fixesUpdate astrocyte yaml to be more informative
Update astrocyte to get the version of the reference genomeUpdate astrocyte yaml to be more informative
Update astrocyte to get the version of the reference genomeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/23Update doi in Readme2020-08-15T09:10:07-05:00Venkat MalladiUpdate doi in Readme[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3899482.svg)](https://doi.org/10.5281/zenodo.3899482)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3899482.svg)](https://doi.org/10.5281/zenodo.3899482)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/22Parallelize tests2020-06-16T09:35:08-05:00Jonathan GesellParallelize testsRe-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Re-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Jonathan GesellJonathan Gesellhttps://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/46Add simple integration CI test2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd simple integration CI testto branches except master and develop to test nextflow run on branchesto branches except master and develop to test nextflow run on branches3.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/28Comparison Script2020-04-25T19:02:01-05:00Venkat MalladiComparison ScriptComparison between current database and updates.Comparison between current database and updates.Venkat MalladiVenkat Malladi