Astrocyte issueshttps://git.biohpc.swmed.edu/groups/BICF/Astrocyte/-/issues2020-11-25T12:08:39-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/28Fix README2020-11-25T12:08:39-06:00Jeremy MathewsFix READMEFix readme instructions for running to clone sra pipeline instead of metagenome analysis pipeline.
Update module versions (singularity and nextflow) in module load command.Fix readme instructions for running to clone sra pipeline instead of metagenome analysis pipeline.
Update module versions (singularity and nextflow) in module load command.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/56Add 5GEXPE/SE as library options2020-11-20T12:13:22-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 5GEXPE/SE as library optionsAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customizedAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customized3.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/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/Astrocyte/methylation_analysis/-/issues/6Add license.2020-12-29T17:33:11-06:00Venkat MalladiAdd license.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/4Update DOI for Methylation pipeline2020-12-29T17:33:19-06:00Venkat MalladiUpdate DOI for Methylation pipeline1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/87Annotation file is missing data2020-08-07T21:10:52-05:00Venkat MalladiAnnotation file is missing dataSymbol is missing in annotation file
Headers are off by oneSymbol is missing in annotation file
Headers are off by one2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/42Update to astrocyte 0.3.12020-07-01T14:35:53-05:00Venkat MalladiUpdate to astrocyte 0.3.1Version 2.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/86Update to astrocyte 0.3.12020-07-01T14:35:06-05:00Venkat MalladiUpdate to astrocyte 0.3.12.0.0Venkat MalladiVenkat Malladihttps://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/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.edu