BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-03-05T09:51:52-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/6Fix design file overwrite2019-03-05T09:51:52-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix design file overwritedesign file gets overwritten during design check
fix by outputting checked design file to new name in .py and .nfdesign file gets overwritten during design check
fix by outputting checked design file to new name in .py and .nfPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/5Add MultiQC2019-08-15T00:29:43-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd MultiQCv1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/4Create output directory option2019-04-27T17:32:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCreate output directory optionPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/3Make instructions2019-04-27T17:31:27-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMake instructionsAdd to readme.mdAdd to readme.mdPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/2Remove reference genome full folder2019-04-27T17:32:34-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove reference genome full folderIn both astrocyte_pkg.yml and main.nfIn both astrocyte_pkg.yml and main.nfPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/1Add cellranger v3.0.12019-02-07T21:05:02-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger v3.0.1Use different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfUse different process depending on version, module loaded by biohpc.config
Remove unnecessary module loads from main.nfPut on Astrocyte Production (1.0.0)Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/28Last 3 steps don't go into user defined output directory2019-04-03T08:15:42-05:00Holly RuessLast 3 steps don't go into user defined output directorydiffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.diffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/27Add Pearson correlation, and make Spearman and Pearson Corr Plots pdf2019-01-31T10:27:28-06:00Holly RuessAdd Pearson correlation, and make Spearman and Pearson Corr Plots pdf1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/26callPeaksMACS exits when data is bad2020-03-15T12:57:14-05:00Holly RuesscallPeaksMACS exits when data is badIn call_peaks_macs.py:
fragment_length = frag_lengths.split(',')[0]
But if the data is bad, then it == 0
Put an if statement to take the second column if the first column is 0In call_peaks_macs.py:
fragment_length = frag_lengths.split(',')[0]
But if the data is bad, then it == 0
Put an if statement to take the second column if the first column is 01.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/25experimentQC plots are empty in PE2019-01-06T09:21:11-06:00Holly RuessexperimentQC plots are empty in PEPE data plots *_fingerprint.png and coverage.png are empty. Works fine for SE dataPE data plots *_fingerprint.png and coverage.png are empty. Works fine for SE data1.0.0https://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/23Use SampleIds/ Experiment Id as file names throughtout pipeline2019-03-10T18:42:13-05:00Venkat MalladiUse SampleIds/ Experiment Id as file names throughtout pipeline1.0.0Venkat MalladiVenkat Malladihttps://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/20invalid option in map_qc.py2019-01-05T22:37:45-06:00Spencer Barnesinvalid option in map_qc.pyLine 190:
"samtools index -@ %d %s" % (cpu_count(), final_bam_filename)
Error thrown that '-@' in an invalid option. Samtools v1.6 manual confirms this is not a valid option for 'samtools index'. Testing whether removing this opti...Line 190:
"samtools index -@ %d %s" % (cpu_count(), final_bam_filename)
Error thrown that '-@' in an invalid option. Samtools v1.6 manual confirms this is not a valid option for 'samtools index'. Testing whether removing this option throws additional errors.https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/10workflow/process_scripts empty after cloning2018-11-02T17:42:27-05:00Holly Ruessworkflow/process_scripts empty after cloningused git clone command to clone RNAseq pipeline. Process_scripts folder is empty and checked on git and noticed that the commit failed.used git clone command to clone RNAseq pipeline. Process_scripts folder is empty and checked on git and noticed that the commit failed.Brandi CantarelBrandi Cantarelhttps://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/18broken link in documentation2019-01-05T22:41:01-06:00Spencer Barnesbroken link in documentationOn Astrocyte website, link to design file template is broken. Error 404.On Astrocyte website, link to design file template is broken. Error 404.1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/9DEA Skip2018-05-16T16:04:11-05:00Jonathan GesellDEA SkipThere is an error in the main.nf when it checks for dea=skip, meaning that it will always run the DEA process.There is an error in the main.nf when it checks for dea=skip, meaning that it will always run the DEA process.Jonathan GesellJonathan Gesell