BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-23T15:51:25-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/44diffbind design file error2020-06-23T15:51:25-05:00Spencer Barnesdiffbind design file errorThe step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would cha...The step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would change the diffbind script to compare Factor or Treatment as default.2.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/1map_reads failure case2020-06-23T16:03:04-05:00Spencer Barnesmap_reads failure caseWhen map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.When map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.Version 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/14Add in peak call with SPP and IDR2020-06-23T15:50:40-05:00Venkat MalladiAdd in peak call with SPP and IDR2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/9Add in blacklist2020-06-23T15:50:34-05:00Venkat MalladiAdd in blacklistAdd blacklist support for mm9,mm10,hg19,hg38Add blacklist support for mm9,mm10,hg19,hg382.0.0Venkat MalladiVenkat Malladihttps://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_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/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_mkfastq/-/issues/41Add test for astrocyte specific run of pipline2020-10-30T11:48:42-05:00Venkat MalladiAdd test for astrocyte specific run of pipline# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701https://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/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/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/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/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_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/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_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 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/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 uploaded