BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-07-31T14:35:46-05:00https://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_mkfastq/-/issues/26Change to cellranger v 3.1.02019-07-31T12:22:09-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduChange to cellranger v 3.1.0v1.3.0Jeremy 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_mkfastq/-/issues/25Add pytest to CI2019-07-22T13:18:32-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd pytest to CIv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/28Add pytest to CI2019-08-15T00:29:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd pytest to CIv1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/27check style2019-07-10T16:55:03-05:00Holly Ruesscheck stylev1.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/24Correct style2019-07-10T16:49:47-05:00Holly RuessCorrect stylev1.2.0Holly RuessHolly Ruesshttps://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/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/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/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 Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/50Change Tests for Peak comparison to be greater than or equal to2019-05-15T10:02:03-05:00Venkat MalladiChange Tests for Peak comparison to be greater than or equal to1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/49check design file failure2019-05-14T15:18:14-05:00Spencer Barnescheck design file failureCurrently check design file step still fails if project is single-end but `fastq_read2` header is not present in design file.Currently check design file step still fails if project is single-end but `fastq_read2` header is not present in design file.1.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/48Single control fails at pool_and_psuedoreplicate2019-05-15T09:29:54-05:00Holly RuessSingle control fails at pool_and_psuedoreplicateThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't workThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't work1.0.4Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/47annotate peaks2020-03-20T23:12:11-05:00Holly Ruessannotate peaksuse gtf file for the annotate peaks step instead of libraries TxDb and orguse gtf file for the annotate peaks step instead of libraries TxDb and org1.1.0Jeremy MathewsJeremy Mathews