BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-13T11:37:11-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/16Move params out of main.nf2020-04-13T11:37:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfWait for astroycte update to handle custom configsWait for astroycte update to handle custom configshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/33New folders for all steps2019-03-16T19:26:26-05:00Venkat MalladiNew folders for all stepsBreak steps into sub-folders by Sample, or Experiment where appropriateBreak steps into sub-folders by Sample, or Experiment where appropriate1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/32Memory2020-06-23T15:56:18-05:00Venkat MalladiMemoryChange Python max mem to maybe 3/4 (test), for samtools sortChange Python max mem to maybe 3/4 (test), for samtools sort3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/14Develop CI2019-08-15T00:29:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDevelop CIastrocyte_cli check
nextflow hu/mu cellranger2/cellranger3 library2/library3 ref1.2.0/ref3.0.0astrocyte_cli check
nextflow hu/mu cellranger2/cellranger3 library2/library3 ref1.2.0/ref3.0.0v1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/cellranger_count/-/issues/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/5Re-direct output2020-01-02T14:24:08-06:00Holly RuessRe-direct outputAdd an option to name the output folderAdd an option to name the output folderVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/30xcor.py, --random-source fails if file is too small2020-03-15T12:56:59-05:00Holly Ruessxcor.py, --random-source fails if file is too smallpossible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' ...possible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' % (tag),
'grep -v "chrM"',
'shuf -n %d --random-source=%s' % (NREADS, tags2)]1.1.0Jeremy MathewsJeremy Mathewshttps://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/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 Cantarel