BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-12-24T21:43:12-06:00https://git.biohpc.swmed.edu/BICF/onboarding/-/issues/11Onboarding document fails to provide BICF Redmine URL2019-12-24T21:43:12-06:00Daniel MoserOnboarding document fails to provide BICF Redmine URLHolly ordered me to submit an issue. She is very serious about Git.
http://bicf.redmine.swmed.eduHolly ordered me to submit an issue. She is very serious about Git.
http://bicf.redmine.swmed.eduVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/92Insert vizapp code2021-08-05T10:22:15-05:00Erand SmakajInsert vizapp codeThe R Scripts for vizapp (server.R and ui.R) seem to contain incorrect code (it contains the HTML for gitlab login page instead of R scripts)
Please substitute with the correct vizapp code.
https://git.biohpc.swmed.edu/BICF/Astrocyte/c...The R Scripts for vizapp (server.R and ui.R) seem to contain incorrect code (it contains the HTML for gitlab login page instead of R scripts)
Please substitute with the correct vizapp code.
https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/tree/dev/vizapphttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/91Update nf-tower token2021-07-25T17:02:51-05:00Venkat MalladiUpdate nf-tower token2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/20Setting singularity to PWD doesnt work in the /work directory.2021-07-22T10:41:35-05:00Jeremy MathewsSetting singularity to PWD doesnt work in the /work directory.Must change nextflow.config to set the singularity directory.Must change nextflow.config to set the singularity directory.https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/30non-biological reads needs renaming2021-07-19T13:42:12-05:00Venkat Malladinon-biological reads needs renamingRejected reads are downloaded but not named appropriatley.Rejected reads are downloaded but not named appropriatley.https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/29Paired-end2021-07-19T13:41:28-05:00Venkat MalladiPaired-endPaired-end is not used anywere in the pipelinesPaired-end is not used anywere in the pipelineshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/23Vm's2021-04-06T08:26:21-05:00Venkat MalladiVm'sAdd list of VM'sAdd list of VM'sVenkat MalladiVenkat Malladihttps://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_mkfastq/-/issues/45Upgrade to cellranger 5.0.02020-11-20T09:57:13-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpgrade to cellranger 5.0.03.0.0Spencer BarnesSpencer Barneshttps://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/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/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_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/cellranger_mkfastq/-/issues/43Add output comments for untarBCL2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd output comments for untarBCLuntarBCL.sh takes FOREVER\
there are 2x `tar -t` before the actual untar\
those `tar -t` take a long time with no stdout updates
need to add echo's for stdout updatesuntarBCL.sh takes FOREVER\
there are 2x `tar -t` before the actual untar\
those `tar -t` take a long time with no stdout updates
need to add echo's for stdout updatesPendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/90Strip spaces in design file2020-12-29T17:26:45-06:00Venkat MalladiStrip spaces in design fileStrip leading or trailing spaces in design fileStrip leading or trailing spaces in design file2.0.0https://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/30Update cancer gene2020-10-19T17:33:19-05:00Venkat MalladiUpdate cancer geneUpdate cancer gene
If IHC says gene (IHC) or gene (Sequencing)Update cancer gene
If IHC says gene (IHC) or gene (Sequencing)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/53Ref 2020-A not compatible with cellrangers < 4.0.02020-11-20T09:47:10-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduRef 2020-A not compatible with cellrangers < 4.0.0# Summary
Selecting 2020-A references with cellranger version < 4.0.0 leads to a ref not found error.
THIS IS A PIPELINE ERROR, NOT COMPATIBLITY WITH CELLRANGER
Users need to be able to use 2020-A refs with cellranger < 4.0.0
# Steps t...# Summary
Selecting 2020-A references with cellranger version < 4.0.0 leads to a ref not found error.
THIS IS A PIPELINE ERROR, NOT COMPATIBLITY WITH CELLRANGER
Users need to be able to use 2020-A refs with cellranger < 4.0.0
# 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/52Generate QC Plot2020-09-18T12:33:29-05:00Jeremy MathewsGenerate QC PlotIn preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for fil...In preparation for a Seurat analysis workflow, the addition of a Violin Plot to display QC for count results can be used to determine inputs for Seurat workflow.
@ghenry has an automated script to determine optimal cutoff values for filtering data. Use the violin plot code below and overlay it with markers of cutoff values.
If values are acceptable, then use "automatic" option in Seurat workflow, else use "manual" and select the cutoffs for filtering data by hand.
"""
VlnPlot(object, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
"""https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/89Diffbind is tsv not csv2020-12-29T17:23:49-06:00Venkat MalladiDiffbind is tsv not csvDiffbind output is actually tsv not csv file forat.Diffbind output is actually tsv not csv file forat.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/42Update to Astocyte 0.4.02020-09-07T06:43:20-05:00Venkat MalladiUpdate to Astocyte 0.4.0# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s18170...# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s181706 @s189701Venkat MalladiVenkat Malladi