cellranger_count issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues2020-11-20T12:13:22-06:00https://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/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/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/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/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/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/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/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/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/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/34Create output plots2020-08-02T09:57:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCreate output plots## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir...## output to:
>output/analysis/*/
## plot:
* PCA with graphclust labels
* tSNE with graphclust labels
* UMAP with graphclust labels
## data for plots in:
>output/count*/*/outs/analysis/
#### remember not to try and read the output dir for the input of the new process... instead in the counts processes add the files necessary to a new outputhttps://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_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.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/40BUG: thread error on Astrocyte2020-04-20T18:31:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduBUG: thread error on AstrocyteDetected by Lavanya (Gupta Lab)...
Exceeding thread limit on Astrocyte intermittently
Appears to be localized to 256v1 nodes (see below, 1574863-1590532)
```
1049334 nf-count3+ FAILED Nucleus024 128GB
1363646 nf-count3+ FAILED Nucleus1...Detected by Lavanya (Gupta Lab)...
Exceeding thread limit on Astrocyte intermittently
Appears to be localized to 256v1 nodes (see below, 1574863-1590532)
```
1049334 nf-count3+ FAILED Nucleus024 128GB
1363646 nf-count3+ FAILED Nucleus156 256GBv1
1432212 nf-count3+ FAILED Nucleus010 128GB
1492005 nf-count3+ NODE_FAIL Nucleus025 128GB
1503055 nf-count3+ FAILED Nucleus059 256GB
1503183 nf-count3+ FAILED Nucleus059 256GB
1574863 nf-count3+ FAILED Nucleus142 256GBv1
1581543 nf-count3+ FAILED Nucleus132 256GBv1
1581544 nf-count3+ FAILED Nucleus193 256GBv1
1581550 nf-count3+ FAILED Nucleus132 256GBv1
1582398 nf-count3+ FAILED Nucleus152 256GBv1
1585588 nf-count3+ FAILED Nucleus140 256GBv1
1590532 nf-count3+ FAILED Nucleus140 256GBv1
```
Where ulimit -u is being reduced for an unknown reason
```
Nucleus140
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1031252
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 4096
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4096
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
```
**FIX**
Add this code to the cellranger process start:
`ulimit -u 16384`v2.1.1https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/41Containerize2020-04-15T21:18:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduContainerizev2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/42Update params to current standards2020-04-15T10:04:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate params to current standardsnon-imputable params do not need to have "param." prefixnon-imputable params do not need to have "param." prefixv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/43Remove unnecessary files from output2020-04-14T10:01:25-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove unnecessary files from outputv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu