BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-08-02T09:57:09-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/35Shiny App2020-08-02T09:57:09-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduShiny App# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs...# Shiny app which recreates count's web_summary.html
## Priority 1
* [x] Select dimentionality reduction type
1. PCA
2. tSNE
3. UMAP
* [x] Select clustering type
1. Graph-Based
2. KMeans 2-10
* [x] Plot
* [x] Show DEGs based on clustering type
## Priority 2
* [ ] Recreate QC page (or find a way to display multi-qc output)
* [ ] Re-calculate Cliff-Knee plot
* Rank order raw_feature_bc_matrix
* Color barcodes from filtered_feature_bc_matrix green... rest redJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/49Add test for astrocyte 0.3.12020-08-02T09:57:17-05:00Venkat MalladiAdd test for astrocyte 0.3.1# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenry# Summary
* [ ] Add test for astrocyte-specific test besides cli
* [ ] Add Badge for astrocyte
* [ ] Test for astrocyte 0.3.1 instead of loading astrocyte
/cc @ghenryGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/16Genomics inventory2020-07-01T20:02:54-05:00Venkat MalladiGenomics inventoryhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/19Move params out of main.nf2019-04-26T15:47:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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 Gesellhttps://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/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/KCE/kce_etl/-/issues/24Add tests Medication2019-12-12T08:30:26-06:00Venkat MalladiAdd tests Medicationhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/24Containerize Pipeline2020-06-17T16:37:54-05:00Jonathan GesellContainerize PipelineDesign the container so that it can be run by Docker as one image.Design the container so that it can be run by Docker as one image.Azure FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/25Add tests radiation2019-12-12T08:30:37-06:00Venkat MalladiAdd tests radiationhttps://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/KCE/kce_etl/-/issues/26Add tests surgery2020-02-07T09:26:16-06:00Venkat MalladiAdd tests surgeryhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/26Fix issue downloading and spliting for single cell data2020-08-21T14:20:59-05:00Venkat MalladiFix issue downloading and spliting for single cell dataThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/27New Beaker code2020-04-25T18:55:13-05:00Venkat MalladiNew Beaker codeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/27Add flag for SAM instead of FastQ2020-08-26T11:06:35-05:00Jonathan GesellAdd flag for SAM instead of FastQCreate an option if users want to download the SAM file instead of the FastQ files.Create an option if users want to download the SAM file instead of the FastQ files.Jonathan GesellJonathan Gesellhttps://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 Malladihttps://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_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/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruess