chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2020-06-23T15:48:58-05:00https://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/chipseq_analysis/-/issues/76Update version of multiqc2020-03-15T12:55:45-05:00Holly RuessUpdate version of multiqcuse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.imguse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/74Annotepeaks2020-06-23T15:49:23-05:00Venkat MalladiAnnotepeaksSeperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.Seperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/70Use specific meme file in motif search2020-12-29T17:30:57-06:00Holly RuessUse specific meme file in motif searchDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip scriptDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip script2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/63Annotate Diffbind output2020-12-29T17:27:14-06:00Holly RuessAnnotate Diffbind outputAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf fileAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf file2.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/60Make both astrocyte compatable and other cluster compatable2020-06-23T15:51:53-05:00Holly RuessMake both astrocyte compatable and other cluster compatableWe need to move the module load from the main.nf into if astrocyte = True statement.We need to move the module load from the main.nf into if astrocyte = True statement.3.0.0Jeremy MathewsJeremy Mathewshttps://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/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/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/51Add in merge request template2019-05-15T13:19:11-05:00Venkat MalladiAdd in merge request templateVenkat 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/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 Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/46Fix Astrocyte links2019-05-15T09:28:20-05:00Holly RuessFix Astrocyte linksLinks from git (for instance design files examples) are not working in AstrocyteLinks from git (for instance design files examples) are not working in Astrocyte1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/45Remove spaces and "weird characters" from design files2019-07-30T09:16:32-05:00Holly RuessRemove spaces and "weird characters" from design files[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file[design.tsv](/uploads/97cb32a15d52c0d7efdff112e1adefd2/design.tsv)
See attached design file. Remove spaces after names and test for weird characters (. - _ ,) to see which programs fail and then remove those at the check design file1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/39Optimizations2020-06-23T15:51:07-05:00Jonathan GesellOptimizationsGeneral speed-ups and optimization of pipeline branches.General speed-ups and optimization of pipeline branches.3.0.0Jonathan GesellJonathan Gesellhttps://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/chipseq_analysis/-/issues/29add plotProfile2020-03-15T12:57:07-05:00Holly Ruessadd plotProfileAdd plotProfile for each sampleAdd plotProfile for each sample1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/22Add defined output folder2019-01-06T09:22:05-06:00Venkat MalladiAdd defined output folder1.0.0https://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/19Add multiqc summary of data2019-04-21T12:06:01-05:00Venkat MalladiAdd multiqc summary of data1.0.0Venkat MalladiVenkat Malladi