BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-04-05T12:09:12-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/3redirect_outputs2019-04-05T12:09:12-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduredirect_outputslook into inputting directory instead of fileslook into inputting directory instead of filesGervaise 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_mkfastq/-/issues/2Optimize mkfastq2019-04-05T12:08:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduOptimize mkfastqGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/1Migrate cellranger_count basics2019-03-28T18:49:50-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMigrate cellranger_count basicsGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/17Update Documentation2019-03-25T10:45:13-05:00Venkat MalladiUpdate DocumentationPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/16Move params out of main.nf2020-04-13T11:37:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfWait for astroycte update to handle custom configsWait for astroycte update to handle custom configshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/33New folders for all steps2019-03-16T19:26:26-05:00Venkat MalladiNew folders for all stepsBreak steps into sub-folders by Sample, or Experiment where appropriateBreak steps into sub-folders by Sample, or Experiment where appropriate1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/32Memory2020-06-23T15:56:18-05:00Venkat MalladiMemoryChange Python max mem to maybe 3/4 (test), for samtools sortChange Python max mem to maybe 3/4 (test), for samtools sort3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/15Add Astrocyte documentation2019-03-24T20:14:37-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd Astrocyte documentationPut on Astrocyte Production (1.0.0)Gervaise 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/chipseq_analysis/-/issues/31skip motif search and diff bind2019-03-12T14:07:41-05:00Holly Ruessskip motif search and diff bindWe don't need to run the analysis all the time. Allow for the skipping of these stepsWe don't need to run the analysis all the time. Allow for the skipping of these steps1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/13Add params from biohpc.config into main.nf2019-03-22T10:37:29-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd params from biohpc.config into main.nfAstrocyte doesn't read params in biohpc.config properly for ref pathAstrocyte doesn't read params in biohpc.config properly for ref pathPut on Astrocyte Production (1.0.0)Gervaise 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.eduhttps://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/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/atacseq_analysis/-/issues/5Re-direct output2020-01-02T14:24:08-06:00Holly RuessRe-direct outputAdd an option to name the output folderAdd an option to name the output folderVersion 2.0Holly RuessHolly Ruesshttps://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/chipseq_analysis/-/issues/30xcor.py, --random-source fails if file is too small2020-03-15T12:56:59-05:00Holly Ruessxcor.py, --random-source fails if file is too smallpossible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' ...possible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' % (tag),
'grep -v "chrM"',
'shuf -n %d --random-source=%s' % (NREADS, tags2)]1.1.0Jeremy MathewsJeremy Mathews