BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-04-12T01:10:42-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/11Speed up fastqc and/or multiqc2019-04-12T01:10:42-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduSpeed up fastqc and/or multiqcAstrocyte Production (v1.0.0)https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/12Move software version report to the bottom2019-04-12T11:36:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove software version report to the bottomAstrocyte Production (v1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/9Split multiqc fastqc by r1/r2/i12019-04-12T11:37:57-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduSplit multiqc fastqc by r1/r2/i1Astrocyte Production (v1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/21Output software versions and methods and references2019-04-18T15:36:36-05:00Venkat MalladiOutput software versions and methods and references1.0.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/34Fix tests for software versions2019-04-20T03:12:15-05:00Venkat MalladiFix tests for software versions1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/24Test Astrocyte2019-04-21T11:41:48-05:00Venkat MalladiTest Astrocyte1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/19Add multiqc summary of data2019-04-21T12:06:01-05:00Venkat MalladiAdd multiqc summary of data1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/35Fix astrocyte run2019-04-22T15:17:51-05:00Venkat MalladiFix astrocyte runAstrocyte is not using the correct variables in Main.nfAstrocyte is not using the correct variables in Main.nf1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/36Update Astrocyte documentation and errors2019-04-22T22:18:14-05:00Venkat MalladiUpdate Astrocyte documentation and errors1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/37Fix software versions test2019-04-22T22:30:59-05:00Venkat MalladiFix software versions test1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/38Missing modules2019-04-23T07:48:40-05:00Venkat MalladiMissing modules1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/13Handle multi-flowcells in fastqc and multiqc2019-04-26T01:34:06-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduHandle multi-flowcells in fastqc and multiqcv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/15Fix astrocyte regex2019-04-26T01:34:28-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix astrocyte regex```
regex: ".*csv"
```
to
```
regex: "*.csv"
``````
regex: ".*csv"
```
to
```
regex: "*.csv"
```v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/14Change location of multiqc config and name2019-04-26T01:34:43-05:00Venkat MalladiChange location of multiqc config and nameCurrent name is .multiqc.yaml should be multiqc.yaml
Also change to location to be under conf directory.Current name is .multiqc.yaml should be multiqc.yaml
Also change to location to be under conf directory.v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/1RNAseq-ProcessScripts2019-04-26T11:07:33-05:00Holly RuessRNAseq-ProcessScriptsWrite instructions on how to make changes to the processScripts for the RNAseq pipeline and link them together in the RNAseq branchWrite instructions on how to make changes to the processScripts for the RNAseq pipeline and link them together in the RNAseq branchHolly RuessHolly Ruesshttps://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/19Change nextflow fastq rename to iterate sample not lane2019-04-26T15:39:36-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange nextflow fastq rename to iterate sample not lanewith large fastq #'s per sample cellranger counts drops some with high lane #'swith large fastq #'s per sample cellranger counts drops some with high lane #'sv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/11Statanal fail at heatmaps2019-04-26T23:12:43-05:00Holly RuessStatanal fail at heatmapsThe dea.R script fails at the heatmap steps. This is caused by either the columnsums or rowsums of the zscore equals zeroThe dea.R script fails at the heatmap steps. This is caused by either the columnsums or rowsums of the zscore equals zeroJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/2Document Backups2019-04-26T23:26:57-05:00Venkat MalladiDocument BackupsVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/18Add DOI2019-04-27T13:11:57-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd DOIWait for 1.1.4 to hit production AstrocyteWait for 1.1.4 to hit production Astrocytev1.2.0Venkat MalladiVenkat Malladi2019-04-22