BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-14T09:53:11-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/38Add 3':5' param2020-04-14T09:53:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 3':5' paramv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/17CI and Nextflow configuration2020-04-13T15:31:27-05:00Venkat MalladiCI and Nextflow configurationVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/82Disk quota exceeded2020-04-13T13:50:12-05:00Venkat MalladiDisk quota exceededVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/18Software Development2020-04-08T09:17:45-05:00Venkat MalladiSoftware DevelopmentVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/11MultiConfig2020-04-04T04:53:22-05:00Jeremy MathewsMultiConfigTest nextflow config to call multiple different config files.
{aws, biohpc, ect.}Test nextflow config to call multiple different config files.
{aws, biohpc, ect.}Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/16Authorship guidelines2020-03-31T12:02:51-05:00Venkat MalladiAuthorship guidelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/28Add percent of reads - mitochondria2020-03-24T14:23:39-05:00Holly RuessAdd percent of reads - mitochondriaDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/73Single Rep Pool and Pseudo2020-03-24T11:46:18-05:00Venkat MalladiSingle Rep Pool and PseudoCheck if for a single rep pool and pseudo replicate works based on new refactored code.Check if for a single rep pool and pseudo replicate works based on new refactored code.1.1.1Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/77Update to Astrocyte 0.2.02020-03-21T11:16:24-05:00Venkat MalladiUpdate to Astrocyte 0.2.0astrocyte/0.2.0astrocyte/0.2.01.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/71hg37 annotate peaks fails2020-03-20T23:12:11-05:00Holly Ruesshg37 annotate peaks failsNeed to fix or remove hg37
Annotate peaks fails with this genomeNeed to fix or remove hg37
Annotate peaks fails with this genome1.1.0https://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/17Move to use Process scripts2020-03-20T23:08:02-05:00Venkat MalladiMove to use Process scriptsVenkat MalladiVenkat Malladihttps://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/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/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/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/65Testing fails on new update2020-03-15T12:56:23-05:00Venkat MalladiTesting fails on new updateTesting fails when adding:
`pytest -m singleend`
`pytest -m pairedend`
For multiple, need to update test orderTesting fails when adding:
`pytest -m singleend`
`pytest -m pairedend`
For multiple, need to update test order1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/66Software References aren't in Multic2020-03-15T12:56:10-05:00Venkat MalladiSoftware References aren't in Multic1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/67Python Version not in Software Version2020-03-15T12:56:03-05:00Venkat MalladiPython Version not in Software Version![Screen_Shot_2019-09-19_at_8.16.13_AM](/uploads/d1f69416b9c4ef171560506c7bcca5d3/Screen_Shot_2019-09-19_at_8.16.13_AM.png)
Update
`
Python': ['version_python.txt', r"python, version (\S+)"],
`![Screen_Shot_2019-09-19_at_8.16.13_AM](/uploads/d1f69416b9c4ef171560506c7bcca5d3/Screen_Shot_2019-09-19_at_8.16.13_AM.png)
Update
`
Python': ['version_python.txt', r"python, version (\S+)"],
`1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/68Remove artifacts2020-03-15T12:55:54-05:00Venkat MalladiRemove artifacts1.1.0Venkat MalladiVenkat Malladi