BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-11-04T10:06:00-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/545GEX QC data not present in multiqc report2020-11-04T10:06:00-06:00Gervaise Henrygervaise.henry@utsouthwestern.edu5GEX QC data not present in multiqc report# Summary
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry# Summary
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/38Add 3':5' param2020-04-14T09:53:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 3':5' paramv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/44Add ability to handle dual index2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to handle dual indexPendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/3Add a changelog2020-12-29T17:33:43-06:00Venkat MalladiAdd a changelog1.0.0https://git.biohpc.swmed.edu/BICF/onboarding/-/issues/7Add Addtional ORCID2019-08-02T10:08:40-05:00Venkat MalladiAdd Addtional ORCIDhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/15Add Astrocyte documentation2019-03-24T20:14:37-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd Astrocyte documentationPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/5Add back tags per process2020-12-29T17:33:34-06:00Venkat MalladiAdd back tags per process1.0.0https://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/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/cellranger_count/-/issues/8Add cellranger 3.0.2 as option2019-03-04T20:43:38-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger 3.0.2 as optionBioHPC in the process of adding cellranger 3.0.2 as a new module versionBioHPC in the process of adding cellranger 3.0.2 as a new module versionPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/55Add cellranger 5.0.02020-11-20T09:57:21-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger 5.0.03.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/9Add cellranger references version 3.0.0 as options2019-03-05T09:51:14-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger references version 3.0.0 as optionsBioHPC in the process of adding to /project/apps_database/cellrangerBioHPC in the process of adding to /project/apps_database/cellrangerPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/1Add cellranger v3.0.12019-02-07T21:05:02-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger v3.0.1Use different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfUse different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/30Add cellranger v 3.1.02019-07-31T14:35:46-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger v 3.1.0* [x] Add process in main.nf
* [x] astrocyte_pkg.yml
* workflow_modules
* workflow_parameters:version
* [x] biohpc.config
* add new process
* [x] .gitlab-ci.yml
* simple1 = count3.1.0
* simple2 = count3.1.0
* detailed1 = count3...* [x] Add process in main.nf
* [x] astrocyte_pkg.yml
* workflow_modules
* workflow_parameters:version
* [x] biohpc.config
* add new process
* [x] .gitlab-ci.yml
* simple1 = count3.1.0
* simple2 = count3.1.0
* detailed1 = count3.1.0
* new detailed2 = copied old detailed1 count3.0.2
* new detailed3 = copied old detailed2 count3.0.1
* new detailed4 = copied old detailed3 count2.1.1
* [x] README.md & index.mdv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/34add checks to checkDesign process2019-11-07T12:44:19-06:00Spencer Barnesadd checks to checkDesign processAdd checks to make sure there are no spaces or extra lines in design file.Add checks to make sure there are no spaces or extra lines in design file.v2.1.5Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/69add checks to determine if fastq files are in proper format and not truncated2020-06-23T15:52:26-05:00Spencer Barnesadd checks to determine if fastq files are in proper format and not truncatedWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidatorWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidator2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/variant_germline/-/issues/1Add CI2019-06-18T11:27:05-05:00Jeremy MathewsAdd CICreate CICreate CIJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/19Add concatination flag2020-04-30T16:16:25-05:00Jonathan GesellAdd concatination flagAdd a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Add a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Astrocyte FunctionalityJonathan GesellJonathan Gesell