BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-23T15:49:10-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/83Unique Experiment check2020-06-23T15:49:10-05:00Venkat MalladiUnique Experiment checkCheck design file for unique experiments and replicates before starting.Check design file for unique experiments and replicates before starting.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/33Untar folder structure2019-09-11T10:46:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUntar folder structureMcDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the...McDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the RTAComplete.txt and if not in just 1 folder... then move the containing folder to to be the root of the process... OR find a way for the process output just to output that parent dirv2.1.5Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/18Update Astrocyte configuration2020-06-01T13:28:24-05:00Venkat MalladiUpdate Astrocyte configuration* [x] email should be `bicf@utsouthwestern.edu`
* [x] Author list: Include Jermey
* [ ] Have Paniz add logo like other pipelines for BICF: https://astrocyte.biohpc.swmed.edu/workflow/browse/
* [x] Update index.html to not reference m...* [x] email should be `bicf@utsouthwestern.edu`
* [x] Author list: Include Jermey
* [ ] Have Paniz add logo like other pipelines for BICF: https://astrocyte.biohpc.swmed.edu/workflow/browse/
* [x] Update index.html to not reference metagenomics pipeline `git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/metagenome_analysis.git`
* [ ] Add release notes
* [x] Fix Jon's email link to his actual email
* [ ] Add in Doc and index.html for display on astrocyte: https://astrocyte.biohpc.swmed.edu/static/docs/workflow_developer/overview.html#docs-user-focused-documentation
* [ ] Add build, nextflow and astrocyte badgesJeremy MathewsJeremy Mathewshttps://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/rnaseq/-/issues/19Update Astrocyte instructions2020-01-07T11:33:51-06:00Venkat MalladiUpdate Astrocyte instructions`One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group``One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group`Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/30Update cancer gene2020-10-19T17:33:19-05:00Venkat MalladiUpdate cancer geneUpdate cancer gene
If IHC says gene (IHC) or gene (Sequencing)Update cancer gene
If IHC says gene (IHC) or gene (Sequencing)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/13update check design file2019-12-09T13:27:55-06:00Holly Ruessupdate check design fileUpdate check design file and add seq lengthUpdate check design file and add seq lengthVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/6Update deeptools2017-10-18T17:22:39-05:00Venkat MalladiUpdate deeptoolsUpdate current deeptools step to incorporate into pipelineUpdate current deeptools step to incorporate into pipeline1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/7Update Documentation2019-05-24T14:17:28-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate DocumentationAstrocyte Production (v1.0.0)Gervaise 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/chipseq_analysis/-/issues/8Update documentation2019-05-06T11:13:09-05:00Venkat MalladiUpdate documentation1.0.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/4Update DOI for Methylation pipeline2020-12-29T17:33:19-06:00Venkat MalladiUpdate DOI for Methylation pipeline1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/23Update doi in Readme2020-08-15T09:10:07-05:00Venkat MalladiUpdate doi in Readme[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3899482.svg)](https://doi.org/10.5281/zenodo.3899482)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3899482.svg)](https://doi.org/10.5281/zenodo.3899482)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/13Update Hourly Help Desk for Subtask2020-02-26T16:14:33-06:00Venkat MalladiUpdate Hourly Help Desk for SubtaskHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/41Update multiqc version/references report2020-07-01T14:36:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Version 2.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/85Update multiqc version/references report2020-06-23T15:48:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/48Update multiqc version/references report2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/40Update multiqc version/references report2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Pendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/72Update multiqc with new singularity images2020-02-12T00:49:35-06:00Venkat MalladiUpdate multiqc with new singularity imageshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/91Update nf-tower token2021-07-25T17:02:51-05:00Venkat MalladiUpdate nf-tower token2.0.0Venkat MalladiVenkat Malladi