databio pepatac issues - Githubissues

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

54 stars 15 forks source link

issues

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signal 11 error with Bowtie2 hg38 alignment

#300 oliviacwhite opened 5 days ago
1
error in pepatac.py script

#299 ASNbioinf opened 6 days ago
4
PERMISSION: download the docker image databio/pepatac

#298 ASNbioinf opened 6 days ago
1
extract peak cleaning into external tool UNTESTED

#297 syntonym opened 1 week ago
1
Consistently report percentages with 4 digits

#296 syntonym closed 1 week ago
1
Extract peak cleaning from `pepatac.py` into a `tools/` script

#295 syntonym opened 2 weeks ago
2
divvy is not using the correct template directory

#294 nsheff closed 1 month ago
1
Reduce verbosity of rerfgenie tag plugin?

#293 nsheff closed 1 month ago
1
Bad error message

#292 nsheff closed 1 month ago
1
PEPATACr.R now gives error with upgraded R dependencies

#291 donaldcampbelljr opened 1 month ago
0
Unable to access jarfile PE

#290 sunta3iouxos closed 3 weeks ago
9
Attempt to fix datatable issue in R

#289 donaldcampbelljr opened 1 month ago
0
Adding a shift with MACS3

#288 nleroy917 closed 1 month ago
2
Upgrade to newest looper, pipestat

#287 donaldcampbelljr closed 1 month ago
0
is the pararead dependency required?

#286 mbassalbioinformatics closed 1 month ago
2
error while running the test pipeline localy

#285 sunta3iouxos closed 1 month ago
4
MACS3 not in the bulker/singularity container

#284 sunta3iouxos closed 1 month ago
5
Update run-conda.md

#283 sunta3iouxos closed 1 month ago
0
v0.11.3 release

#282 donaldcampbelljr closed 5 months ago
0
Getting a Python pipestat error: cannot import name 'get_file_for_project'

#281 ndrubins closed 5 months ago
3
problem opening file: -B in preseq with ./configure --enable-hts option

#280 h20gg702 opened 7 months ago
4
The production of *peaks_rmBlacklist.narrowPeak files

#279 tan200000000 opened 8 months ago
1
collapsePeaks fails during project level execution of tutorial

#278 DavideBrex opened 8 months ago
0
runp fails when running the tutorial

#277 DavideBrex closed 8 months ago
7
'Pipestat compatible': False, 'Commands submitted': '0 of 8', 'Jobs submitted': 0

#276 ChangshengWei97 closed 1 month ago
4
Error: Install the "PEPATACr" R package before proceeding.

#275 DavideBrex closed 8 months ago
2
The count table with a PEPATAC-produced consensus peak set is incorrect.

#274 zhongzheng1999 closed 6 months ago
0
The peakCounts function in PEPATACr.R should probably need fixing

#273 zhongzheng1999 closed 6 months ago
1
Issues with Result Aggregation in looper runp and looper report！

#272 zhongzheng1999 closed 6 months ago
1
The samples cannot be separated in the result file

#271 zhongzheng1999 closed 9 months ago
2
pypiper.exceptions.SubprocessError: Subprocess returned nonzero result.

#270 zhongzheng1999 closed 9 months ago
1
v0.11.2 release

#269 donaldcampbelljr closed 10 months ago
0
fastqc links do not work in report

#268 donaldcampbelljr closed 10 months ago
1
looper runp looper.pep_config output None --solved

#267 miximimi closed 10 months ago
2
NameError: name '_LOGGER' is not defined

#266 atraunbauer opened 10 months ago
4
v0.11.1

#265 donaldcampbelljr closed 10 months ago
0
Error when running project level pipeline: Error in data.table::rbindlist(sapply(project_samples, FUN = yamlToDT, : Item 1 of input is not a data.frame, data.table or list

#264 donaldcampbelljr closed 10 months ago
3
Add documentation clarity to rerunning pipelines

#263 donaldcampbelljr closed 10 months ago
0
problem rerun using looper and Error in opt_get_verb() -- solved

#262 miximimi opened 10 months ago
3
v0.11.0 Release

#261 donaldcampbelljr closed 11 months ago
0
Run PEPATAC on a PEP on PEPHUB

#260 donaldcampbelljr opened 11 months ago
0
Using `looper runp` for PEPATAC Collator with Looper pre-release (1.6.0) results in errors

#259 donaldcampbelljr closed 12 months ago
2
running PEPATAC example shows float(pm.get_stat("Raw_reads")) error, float() argument must be a string or a real number, not 'NoneType'

#258 yitaoyitaoyitao closed 10 months ago
5
Separate stats.yaml vs unified results.yaml

#257 donaldcampbelljr closed 10 months ago
2
Unable to create html reports using looper report when using newest looper (>1.5.0)

#256 donaldcampbelljr closed 10 months ago
9
Dev test new looper, pypiper, pipestat

#255 donaldcampbelljr closed 11 months ago
1
PEPATAC incompatible with pypiper stats.yaml file

#254 DQ-Zhang closed 10 months ago
1
There are still overlapping peaks in the *_peaks_normalized.narrowPeak file for samples and in produced consensus peak set for project

#253 yqlan opened 1 year ago
0
How to set my own adapter file?

#252 yqlan opened 1 year ago
0
how can i run `looper run` without creating env variable '$REFGENIE'

#251 yqlan opened 1 year ago
2