databio pepatac issues - Githubissues

databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing

http://pepatac.databio.org

BSD 2-Clause "Simplified" License

51 stars 13 forks source link

issues

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v0.11.3 release

#282 donaldcampbelljr closed 1 month ago
0
Getting a Python pipestat error: cannot import name 'get_file_for_project'

#281 ndrubins closed 1 month ago
3
problem opening file: -B in preseq with ./configure --enable-hts option

#280 h20gg702 opened 2 months ago
0
The production of *peaks_rmBlacklist.narrowPeak files

#279 tan200000000 opened 3 months ago
1
collapsePeaks fails during project level execution of tutorial

#278 DavideBrex opened 3 months ago
0
runp fails when running the tutorial

#277 DavideBrex closed 3 months ago
7
'Pipestat compatible': False, 'Commands submitted': '0 of 8', 'Jobs submitted': 0

#276 ChangshengWei97 opened 3 months ago
3
Error: Install the "PEPATACr" R package before proceeding.

#275 DavideBrex closed 3 months ago
2
The count table with a PEPATAC-produced consensus peak set is incorrect.

#274 zhongzheng1999 closed 1 month ago
0
The peakCounts function in PEPATACr.R should probably need fixing

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

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

#271 zhongzheng1999 closed 5 months ago
2
pypiper.exceptions.SubprocessError: Subprocess returned nonzero result.

#270 zhongzheng1999 closed 5 months ago
1
v0.11.2 release

#269 donaldcampbelljr closed 5 months ago
0
fastqc links do not work in report

#268 donaldcampbelljr closed 5 months ago
1
looper runp looper.pep_config output None --solved

#267 miximimi closed 5 months ago
2
NameError: name '_LOGGER' is not defined

#266 atraunbauer opened 5 months ago
4
v0.11.1

#265 donaldcampbelljr closed 5 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 5 months ago
3
Add documentation clarity to rerunning pipelines

#263 donaldcampbelljr closed 5 months ago
0
problem rerun using looper and Error in opt_get_verb() -- solved

#262 miximimi opened 5 months ago
3
v0.11.0 Release

#261 donaldcampbelljr closed 6 months ago
0
Run PEPATAC on a PEP on PEPHUB

#260 donaldcampbelljr opened 6 months ago
0
Using `looper runp` for PEPATAC Collator with Looper pre-release (1.6.0) results in errors

#259 donaldcampbelljr closed 7 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 5 months ago
5
Separate stats.yaml vs unified results.yaml

#257 donaldcampbelljr closed 5 months ago
2
Unable to create html reports using looper report when using newest looper (>1.5.0)

#256 donaldcampbelljr closed 5 months ago
9
Dev test new looper, pypiper, pipestat

#255 donaldcampbelljr closed 6 months ago
1
PEPATAC incompatible with pypiper stats.yaml file

#254 DQ-Zhang closed 5 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 8 months ago
0
How to set my own adapter file?

#252 yqlan opened 8 months ago
0
how can i run `looper run` without creating env variable '$REFGENIE'

#251 yqlan opened 9 months ago
1
Skipping 1 packages not available: pepr

#250 TianJie327 opened 9 months ago
0
Not remove duplicates

#249 gbloeb opened 10 months ago
0
looper bug. I change looper version from 1.4.3 to 1.3.0. How can I debug? Please help, thanks!!!!

#248 Conskier opened 11 months ago
1
update looper reqs for point release v0.10.5

#247 donaldcampbelljr closed 11 months ago
0
PEPATAC with looper failed with the latest looper and eido

#246 xuebingjie1990 opened 11 months ago
5
Traceback error when running looper for tutorial data

#245 beginnertobioinformatics closed 11 months ago
4
eido 0.2.0 has changes that break pepatac

#244 molecules closed 11 months ago
1
There’s NO JAVA in docker image

#243 victorwang123 opened 1 year ago
0
About Run PEPATAC in a container

#242 victorwang123 opened 1 year ago
0
conda install: pip failed, No matching distribution found for codecov==2.1.12

#241 ShannonTown closed 1 year ago
3
Problem with refgenie

#240 peculiar97 closed 1 year ago
2
Error installing PEPATAC in conda environment || PackageNotFound

#239 unikill066 opened 1 year ago
0
lock file Problem

#238 AnthonyPhosphate opened 1 year ago
1
tutorial to run from singularity is failing with this error:The following required tool(s) are not callable: macs2

#237 bioarpit1 opened 1 year ago
2
Problem in creating consensus ATAC peaks

#236 gauriprasad08 opened 1 year ago
3
TSSE score appropriate cutoff

#235 ksmtnals90 opened 1 year ago
0
Fastq filter_paired_fq.pl function did not complete successfully

#234 ksmtnals90 opened 1 year ago
0
columns in ref_peaks_coverage.bed

#233 cristanchoa opened 1 year ago
1