cellranger_count issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues2019-03-10T17:00:53-05:00https://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.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/9Add cellranger references version 3.0.0 as options2019-03-05T09:51:14-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger references version 3.0.0 as optionsBioHPC in the process of adding to /project/apps_database/cellrangerBioHPC in the process of adding to /project/apps_database/cellrangerPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/8Add cellranger 3.0.2 as option2019-03-04T20:43:38-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger 3.0.2 as optionBioHPC in the process of adding cellranger 3.0.2 as a new module versionBioHPC in the process of adding cellranger 3.0.2 as a new module versionPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/7Fix config file2019-03-05T09:50:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix config fileAdd executor to processes
Add min memory (memory '120GB') to cellranger processes (cellranger requires 6GB per core)Add executor to processes
Add min memory (memory '120GB') to cellranger processes (cellranger requires 6GB per core)Put on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/4Create output directory option2019-04-27T17:32:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCreate output directory optionPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/2Remove reference genome full folder2019-04-27T17:32:34-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove reference genome full folderIn both astrocyte_pkg.yml and main.nfIn both astrocyte_pkg.yml and main.nfPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/1Add cellranger v3.0.12019-02-07T21:05:02-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger v3.0.1Use different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfUse different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfPut on Astrocyte Production (1.0.0)Gervaise 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/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/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 Mathews