BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-07-18T16:18:45-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/6Docker Image Integration2019-07-18T16:18:45-05:00Jonathan GesellDocker Image IntegrationTest for integrating Docker imagesTest for integrating Docker imagesJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/58Single control or experiment fails at call peaks macs2020-03-15T12:56:31-05:00Holly RuessSingle control or experiment fails at call peaks macsThe error is noticed at callpeaksmacs when a bedpe is an input instead of a tagAlign file.
The error is actually in the pool and pseudoreplicates stepThe error is noticed at callpeaksmacs when a bedpe is an input instead of a tagAlign file.
The error is actually in the pool and pseudoreplicates step1.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/5Correct config2019-07-05T10:01:11-05:00Jonathan GesellCorrect configCorrecting the config files for Astrocyte and general deploymentCorrecting the config files for Astrocyte and general deploymentJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/6ADD TO2019-11-15T10:34:11-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduADD TOHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/57Broken citation link2019-07-09T08:58:33-05:00Holly RuessBroken citation linkFix the broken citation link. references.txt was deleted; use the mdFix the broken citation link. references.txt was deleted; use the md1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/16CheckDesignFile process2019-07-08T21:20:43-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCheckDesignFile processnextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypas...nextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypass that to run on a super by:
```
process checkdesignfile {
queue 'super'
...
```Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/variant_germline/-/issues/2Fix SubModules2019-06-11T11:10:15-05:00Jeremy MathewsFix SubModulespossible solution: https://docs.gitlab.com/ee/ci/git_submodules.htmlpossible solution: https://docs.gitlab.com/ee/ci/git_submodules.htmlJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/variant_germline/-/issues/1Add CI2019-06-18T11:27:05-05:00Jeremy MathewsAdd CICreate CICreate CIJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/15Check file inputs2019-07-08T21:20:43-05:00Jeremy MathewsCheck file inputscheck for ".fq" or ".fastq" and gzip files to ".gz" formatcheck for ".fq" or ".fastq" and gzip files to ".gz" formatJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/14Fix CI2019-06-11T16:36:00-05:00Jeremy MathewsFix CIFix CI to remove bugs and run through checksFix CI to remove bugs and run through checksJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/56reference fasta file has wrong name2019-05-31T08:29:33-05:00Holly Ruessreference fasta file has wrong nameReference fasta file used in memechip is called genome.fa.txt. This appears in the main.nf file and may elsewhere. It should be genome.fa.
Also, since this error in memechip produces non-emptyp output files but the files are errors. We ...Reference fasta file used in memechip is called genome.fa.txt. This appears in the main.nf file and may elsewhere. It should be genome.fa.
Also, since this error in memechip produces non-emptyp output files but the files are errors. We need to integrate a solution to check if these files are not only produced and not empty, but that the contents of the files are correct1.0.6Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/23Move untarBCL code into a bash script2019-05-24T14:16:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove untarBCL code into a bash scriptmove the code from the process into 1 *or* 2 bash scripts in the ./workflow/scripts folder
either 1 script which tests for spaces and another one to run the untar... or 1 with both... @s189701, you decide...move the code from the process into 1 *or* 2 bash scripts in the ./workflow/scripts folder
either 1 script which tests for spaces and another one to run the untar... or 1 with both... @s189701, you decide...v1.2.0Jeremy 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/tcga_shiny/-/issues/2remove legend from boxplots2019-05-24T12:51:39-05:00Spencer Barnesremove legend from boxplotsLegend is redundant. Should remove from plot.Legend is redundant. Should remove from plot.1.0.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/tcga_shiny/-/issues/1blank page on survival plot download2019-05-22T16:59:37-05:00Spencer Barnesblank page on survival plot downloadWhen downloading the survival plot, a blank page is printed into the pdf file before the plot.When downloading the survival plot, a blank page is printed into the pdf file before the plot.1.0.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/55Fail Pipeline if less reads map to genome2019-07-10T09:13:01-05:00Jeremy MathewsFail Pipeline if less reads map to genomePipeline fails due to selecting incorrect genome or bad fastq files. Currently runs pipeline till callPeaks. Add error check in mapPeaks to compare minimum mapped to percentage. Output possible reasons to output file.Pipeline fails due to selecting incorrect genome or bad fastq files. Currently runs pipeline till callPeaks. Add error check in mapPeaks to compare minimum mapped to percentage. Output possible reasons to output file.1.0.6Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/5Astrocyte documentation update2019-05-18T10:46:27-05:00Venkat MalladiAstrocyte documentation updateVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/54License spacing2019-05-17T13:51:10-05:00Venkat MalladiLicense spacingVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/53Add license2019-05-17T12:19:47-05:00Venkat MalladiAdd licenseAdd MIT license documentation to all parts of the codeAdd MIT license documentation to all parts of the codeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/52Astrocyte Bug Fixes2019-05-16T09:10:45-05:00Venkat MalladiAstrocyte Bug Fixes- Fix generalized tests
- Links in astrocyte- Fix generalized tests
- Links in astrocyte1.0.4Venkat MalladiVenkat Malladi