BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2021-04-13T12:31:12-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/17Statanal Fail on single replicate2021-04-13T12:31:12-05:00Jeremy MathewsStatanal Fail on single replicateSkip statanal if # of samples is less than 2Skip statanal if # of samples is less than 2Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/30Add multiqc output to CI artifacts2019-08-14T23:31:42-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd multiqc output to CI artifactsv1.3.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/36MultiQC error2019-08-13T21:25:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMultiQC errorcellranger count outputs thousands with a comma surrounded by quotes:
[metrics_summary.csv](/uploads/bf7663f603940a9dbfb96b3160d4771f/metrics_summary.csv)
The count processes convert the csv to tsv:
```
sed -E 's/("([^"]*)")?,/\\2\t/g' ...cellranger count outputs thousands with a comma surrounded by quotes:
[metrics_summary.csv](/uploads/bf7663f603940a9dbfb96b3160d4771f/metrics_summary.csv)
The count processes convert the csv to tsv:
```
sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
```
The sed is splitting the comma in the last comma:
[BPH389PrGF_metrics_summary.tsv](/uploads/20184c06a382db3e20af3ce0af99b2cb/BPH389PrGF_metrics_summary.tsv)
That makes multiqc have throws an error because it's seeing an extra column
[.command.log](/uploads/c21552c1ce8661c4437aed92b15e9641/.command.log)
[multiqc_report.html](/uploads/3e8f11ff09e7b37e13d46656b416608f/multiqc_report.html)v1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/29Fix CountDesign2019-08-05T11:16:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix CountDesign1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)v1.3.0Jeremy MathewsJeremy Mathewshttps://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/33Exclude changes in *.md for CI2019-07-31T23:55:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduExclude changes in *.md for CIexcept:
changes:
- "*.md"except:
changes:
- "*.md"Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/28Exclude changes in *.md for CI2019-07-31T23:55:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduExclude changes in *.md for CIexcept:
changes:
- "*.md"except:
changes:
- "*.md"Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/62Filter reads increase memory2020-12-29T17:30:29-06:00Venkat MalladiFilter reads increase memoryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retry2.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/27Add more artifacts to CI2019-07-31T12:31:14-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd more artifacts to CI* multiqc_report.html* multiqc_report.htmlv1.3.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/32Add more artifacts to CI2019-07-31T14:35:47-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd more artifacts to CI* web_summary.html
* multiqc_report.html* web_summary.html
* multiqc_report.htmlv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/31Add human mouse mix reference v3.1.02019-07-31T14:35:46-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd human mouse mix reference v3.1.0Changes needed:
* [x] astrocyte_pkg.yml
* code has to be: GRCh38-and-mm10-3.1.0
* text should be 'Human GRCh38 + Mouse GRCm38 (mm10) release 93'
* put it directly above the two other human mouse mixes
* *NOTE: please fix mm19 to mm10*
...Changes needed:
* [x] astrocyte_pkg.yml
* code has to be: GRCh38-and-mm10-3.1.0
* text should be 'Human GRCh38 + Mouse GRCm38 (mm10) release 93'
* put it directly above the two other human mouse mixes
* *NOTE: please fix mm19 to mm10*
* [x] biohpc.config
* In params:genomes: add the code from astrocyte_pkg.yml translation to physical location than Paniz will hopefully be making for us (see slack message)
* [x] README.md & index.mdv1.2.0Jeremy MathewsJeremy Mathewshttps://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/26Change to cellranger v 3.1.02019-07-31T12:22:09-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange to cellranger v 3.1.0v1.3.0Jeremy MathewsJeremy Mathewshttps://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/29Test for kitVersion=3 and version=2.1.1 and exit if true2019-07-23T19:45:59-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduTest for kitVersion=3 and version=2.1.1 and exit if truev1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/25Add pytest to CI2019-07-22T13:18:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd pytest to CIv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/28Add pytest to CI2019-08-15T00:29:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd pytest to CIv1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/61add python version to multiqc process2019-07-19T08:32:16-05:00Spencer Barnesadd python version to multiqc processCurrently, the multiqc html does not list the python version used in the pipeline. Main.nf should be modified to produce a 'version_python.txt' file and the generate_versions.py should be modified such that its output, 'software versions...Currently, the multiqc html does not list the python version used in the pipeline. Main.nf should be modified to produce a 'version_python.txt' file and the generate_versions.py should be modified such that its output, 'software versions', includes the python version.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/60Make both astrocyte compatable and other cluster compatable2020-06-23T15:51:53-05:00Holly RuessMake both astrocyte compatable and other cluster compatableWe need to move the module load from the main.nf into if astrocyte = True statement.We need to move the module load from the main.nf into if astrocyte = True statement.3.0.0Jeremy MathewsJeremy Mathews