cellranger_count issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues2020-08-14T14:01:39-05:00https://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/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.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/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/39AWSify2020-02-21T13:10:52-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWSifyv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/38Add 3':5' param2020-04-14T09:53:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 3':5' paramv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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_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_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_count/-/issues/26Move module load into nextflow process2019-05-24T14:12:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove module load into nextflow processsee cellranger_mkfastq for examplesee cellranger_mkfastq for examplev1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/25Add error checking for filename/folder names2019-05-24T14:16:03-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd error checking for filename/folder namesv1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/24Organize output folders2019-05-03T21:47:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduOrganize output folderseg check design into misc foldereg check design into misc folderv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/23CI: mkdir ln forcing2019-08-15T00:30:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCI: mkdir ln forcingmkdir -p
ln -sfnmkdir -p
ln -sfnv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/21Change regex in astrocyte yaml2019-08-15T00:30:07-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange regex in astrocyte yamlrelated to BICF/Astrocyte/cellranger_mkfastq#16related to BICF/Astrocyte/cellranger_mkfastq#16v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/18Change process selector2019-04-26T15:39:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange process selector- remove redundant process name out of tag
- update to fix: **WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$count301 = <value>` with a process selector**- remove redundant process name out of tag
- update to fix: **WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$count301 = <value>` with a process selector**v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/14Develop CI2019-08-15T00:29:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelop CIastrocyte_cli check
nextflow hu/mu cellranger2/cellranger3 library2/library3 ref1.2.0/ref3.0.0astrocyte_cli check
nextflow hu/mu cellranger2/cellranger3 library2/library3 ref1.2.0/ref3.0.0v1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/12Make param.genomeLocation have full path2019-03-10T17:00:53-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMake param.genomeLocation have full pathSo custom refs can be used on CLI without editing biohpc.configSo custom refs can be used on CLI without editing biohpc.configPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/11Add parameter for 10x kit version2019-03-05T18:47:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd parameter for 10x kit versionauto, v3, v2auto, v3, v2Put on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu