databio/pepatac issues and pull requests

#296 - Consistently report percentages with 4 digits

Pull Request - State: closed - Opened by syntonym 8 days ago - 1 comment

#295 - Extract peak cleaning from `pepatac.py` into a `tools/` script

Issue - State: open - Opened by syntonym 8 days ago - 2 comments
Labels: enhancement

#294 - divvy is not using the correct template directory

Issue - State: closed - Opened by nsheff about 1 month ago - 1 comment
Labels: bug, priority - high

#293 - Reduce verbosity of rerfgenie tag plugin?

Issue - State: closed - Opened by nsheff about 1 month ago - 1 comment
Labels: docs

#292 - Bad error message

Issue - State: closed - Opened by nsheff about 1 month ago - 1 comment
Labels: docs

#291 - PEPATACr.R now gives error with upgraded R dependencies

Issue - State: open - Opened by donaldcampbelljr about 1 month ago

#290 - Unable to access jarfile PE

Issue - State: closed - Opened by sunta3iouxos about 1 month ago - 9 comments

#289 - Attempt to fix datatable issue in R

Pull Request - State: open - Opened by donaldcampbelljr about 1 month ago

#288 - Adding a shift with MACS3

Issue - State: closed - Opened by nleroy917 about 1 month ago - 2 comments

#287 - Upgrade to newest looper, pipestat

Pull Request - State: closed - Opened by donaldcampbelljr about 1 month ago

#286 - is the pararead dependency required?

Issue - State: closed - Opened by mbassalbioinformatics about 2 months ago - 2 comments

#285 - error while running the test pipeline localy

Issue - State: closed - Opened by sunta3iouxos about 2 months ago - 4 comments
Labels: likely-solved

#284 - MACS3 not in the bulker/singularity container

Issue - State: closed - Opened by sunta3iouxos about 2 months ago - 5 comments
Labels: likely-solved

#283 - Update run-conda.md

Pull Request - State: closed - Opened by sunta3iouxos 3 months ago

#282 - v0.11.3 release

Pull Request - State: closed - Opened by donaldcampbelljr 5 months ago

#281 - Getting a Python pipestat error: cannot import name 'get_file_for_project'

Issue - State: closed - Opened by ndrubins 6 months ago - 3 comments

#280 - problem opening file: -B in preseq with ./configure --enable-hts option

Issue - State: open - Opened by h20gg702 7 months ago - 4 comments
Labels: awaiting-response

#279 - The production of *peaks_rmBlacklist.narrowPeak files

Issue - State: open - Opened by tan200000000 8 months ago - 1 comment

#278 - collapsePeaks fails during project level execution of tutorial

Issue - State: open - Opened by DavideBrex 8 months ago

#277 - runp fails when running the tutorial

Issue - State: closed - Opened by DavideBrex 8 months ago - 7 comments

#276 - 'Pipestat compatible': False, 'Commands submitted': '0 of 8', 'Jobs submitted': 0

Issue - State: closed - Opened by ChangshengWei97 8 months ago - 4 comments

#275 - Error: Install the "PEPATACr" R package before proceeding.

Issue - State: closed - Opened by DavideBrex 8 months ago - 2 comments

#274 - The count table with a PEPATAC-produced consensus peak set is incorrect.

Issue - State: closed - Opened by zhongzheng1999 9 months ago

#273 - The peakCounts function in PEPATACr.R should probably need fixing

Issue - State: closed - Opened by zhongzheng1999 9 months ago - 1 comment

#272 - Issues with Result Aggregation in looper runp and looper report！

Issue - State: closed - Opened by zhongzheng1999 9 months ago - 1 comment

#271 - The samples cannot be separated in the result file

Issue - State: closed - Opened by zhongzheng1999 10 months ago - 2 comments

#270 - pypiper.exceptions.SubprocessError: Subprocess returned nonzero result.

Issue - State: closed - Opened by zhongzheng1999 10 months ago - 1 comment

#269 - v0.11.2 release

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago

#268 - fastqc links do not work in report

Issue - State: closed - Opened by donaldcampbelljr 10 months ago - 1 comment
Labels: likely-solved

#267 - looper runp looper.pep_config output None --solved

Issue - State: closed - Opened by miximimi 10 months ago - 2 comments

#266 - NameError: name '_LOGGER' is not defined

Issue - State: open - Opened by atraunbauer 10 months ago - 4 comments

#265 - v0.11.1

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago

#264 - 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

Issue - State: closed - Opened by donaldcampbelljr 10 months ago - 3 comments

#263 - Add documentation clarity to rerunning pipelines

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago

#262 - problem rerun using looper and Error in opt_get_verb() -- solved

Issue - State: open - Opened by miximimi 10 months ago - 3 comments
Labels: likely-solved

#261 - v0.11.0 Release

Pull Request - State: closed - Opened by donaldcampbelljr 11 months ago

#260 - Run PEPATAC on a PEP on PEPHUB

Issue - State: open - Opened by donaldcampbelljr 11 months ago

#259 - Using `looper runp` for PEPATAC Collator with Looper pre-release (1.6.0) results in errors

Issue - State: closed - Opened by donaldcampbelljr 12 months ago - 2 comments
Labels: likely-solved

#258 - running PEPATAC example shows float(pm.get_stat("Raw_reads")) error, float() argument must be a string or a real number, not 'NoneType'

Issue - State: closed - Opened by yitaoyitaoyitao 12 months ago - 5 comments
Labels: likely-solved

#257 - Separate stats.yaml vs unified results.yaml

Issue - State: closed - Opened by donaldcampbelljr 12 months ago - 2 comments
Labels: likely-solved

#256 - Unable to create html reports using looper report when using newest looper (>1.5.0)

Issue - State: closed - Opened by donaldcampbelljr about 1 year ago - 9 comments
Labels: likely-solved

#255 - Dev test new looper, pypiper, pipestat

Pull Request - State: closed - Opened by donaldcampbelljr about 1 year ago - 1 comment

#254 - PEPATAC incompatible with pypiper stats.yaml file

Issue - State: closed - Opened by DQ-Zhang about 1 year ago - 1 comment
Labels: priority - high

#253 - There are still overlapping peaks in the *_peaks_normalized.narrowPeak file for samples and in produced consensus peak set for project

Issue - State: open - Opened by yqlan about 1 year ago

#252 - How to set my own adapter file?

Issue - State: open - Opened by yqlan about 1 year ago

#251 - how can i run `looper run` without creating env variable '$REFGENIE'

Issue - State: open - Opened by yqlan about 1 year ago - 2 comments

#250 - Skipping 1 packages not available: pepr

Issue - State: closed - Opened by TianJie327 about 1 year ago - 1 comment

#249 - Not remove duplicates

Issue - State: open - Opened by gbloeb about 1 year ago

#248 - looper bug. I change looper version from 1.4.3 to 1.3.0. How can I debug? Please help, thanks!!!!

Issue - State: closed - Opened by Conskier over 1 year ago - 2 comments

#247 - update looper reqs for point release v0.10.5

Pull Request - State: closed - Opened by donaldcampbelljr over 1 year ago

#246 - PEPATAC with looper failed with the latest looper and eido

Issue - State: open - Opened by xuebingjie1990 over 1 year ago - 5 comments

#245 - Traceback error when running looper for tutorial data

Issue - State: closed - Opened by beginnertobioinformatics over 1 year ago - 4 comments

#244 - eido 0.2.0 has changes that break pepatac

Issue - State: closed - Opened by molecules over 1 year ago - 1 comment

#243 - There’s NO JAVA in docker image

Issue - State: open - Opened by victorwang123 over 1 year ago

#242 - About Run PEPATAC in a container

Issue - State: open - Opened by victorwang123 over 1 year ago

#241 - conda install: pip failed, No matching distribution found for codecov==2.1.12

Issue - State: closed - Opened by ShannonTown over 1 year ago - 3 comments

#240 - Problem with refgenie

Issue - State: closed - Opened by peculiar97 over 1 year ago - 2 comments

#239 - Error installing PEPATAC in conda environment || PackageNotFound

Issue - State: open - Opened by unikill066 over 1 year ago - 1 comment

#238 - lock file Problem

Issue - State: open - Opened by AnthonyPhosphate over 1 year ago - 1 comment

#237 - tutorial to run from singularity is failing with this error:The following required tool(s) are not callable: macs2

Issue - State: open - Opened by bioarpit1 over 1 year ago - 2 comments

#236 - Problem in creating consensus ATAC peaks

Issue - State: open - Opened by gauriprasad08 over 1 year ago - 3 comments

#235 - TSSE score appropriate cutoff

Issue - State: open - Opened by ksmtnals90 over 1 year ago

#234 - Fastq filter_paired_fq.pl function did not complete successfully

Issue - State: open - Opened by ksmtnals90 over 1 year ago

#233 - columns in ref_peaks_coverage.bed

Issue - State: open - Opened by cristanchoa about 2 years ago - 1 comment

#232 - Error at "TSS distance distribution" step

Issue - State: open - Opened by marta-nazzari about 2 years ago

#231 - Issue submitting samples with alternate genomes

Issue - State: open - Opened by rylanci about 2 years ago - 5 comments

#230 - hg38 not exported object from namespace:GenomicDistributionsData

Issue - State: open - Opened by kloot about 2 years ago - 2 comments

#229 - R.utils not in requirements

Issue - State: open - Opened by nsheff about 2 years ago - 2 comments
Labels: bug

#228 - argparser is not in requirements

Issue - State: open - Opened by nsheff about 2 years ago - 1 comment
Labels: bug

#227 - docker image is missing R packages

Issue - State: open - Opened by nsheff about 2 years ago

#226 - checkinstall bugs

Issue - State: open - Opened by nsheff about 2 years ago - 1 comment

#225 - Where are Supplemental Files 1..4 ?

Issue - State: closed - Opened by kloot about 2 years ago - 1 comment

#224 - Installation conflict with fseq

Issue - State: open - Opened by AnthonyPhosphate about 2 years ago - 3 comments

#223 - Error on single end data

Issue - State: open - Opened by lmckinno about 2 years ago - 1 comment

#222 - Cannot run pepatac through docker, conda, or singularity

Issue - State: open - Opened by prm123342 about 2 years ago

#221 - Test run fails with this error: skewer (0.2.2): Can not read adapter sequences from FASTA file "tools/NexteraPE-PE.fa"

Issue - State: closed - Opened by ybukhman over 2 years ago - 2 comments

#220 - Is there any way to specify the alignment output should be in cram format?

Issue - State: open - Opened by vulpescu over 2 years ago

#219 - Unable to generate count table with reference peaks

Issue - State: open - Opened by gbloeb over 2 years ago - 4 comments

#218 - Unable to generate counts table for consensus peaks (pipeline ignores _ref_peaks_coverage.bed files)

Issue - State: open - Opened by kathleenabadie over 2 years ago

#217 - Is there a way to run IDR with pepatac?

Issue - State: open - Opened by imk1 almost 3 years ago

#216 - TypeError

Issue - State: open - Opened by namzoo99 almost 3 years ago - 11 comments

#215 - Documenting way to run pipeline to generate reads in reference peak set

Issue - State: open - Opened by gbloeb almost 3 years ago

#214 - Specifying genome size in config.yaml

Issue - State: closed - Opened by gbloeb almost 3 years ago - 3 comments

#213 - PEPATACr no longer available

Issue - State: closed - Opened by gbloeb almost 3 years ago - 2 comments

#212 - Singularity Issue

Issue - State: open - Opened by e-arslan almost 3 years ago

#211 - update hitaggregator function

Pull Request - State: open - Opened by ccrobertson almost 3 years ago - 1 comment

#210 - Problems with checkinstall for conda installation and pipeline failure

Issue - State: open - Opened by ndrdenny almost 3 years ago - 3 comments

#209 - PEPATACr::createStatsSummary Error

Issue - State: open - Opened by hadgie almost 3 years ago - 8 comments

#205 - Problem with parsing of chromosome names that contain | symbol

Issue - State: closed - Opened by khorms about 3 years ago - 1 comment

#204 - TSS_hg38 not available in GenomicDistributions package and GenomicDistributionsData package is not installed

Issue - State: closed - Opened by hiroyukikato911 about 3 years ago - 1 comment

#203 - Question about rCRSd and human_repeats

Issue - State: open - Opened by hiroyukikato911 about 3 years ago - 1 comment

#201 - quantitative ATACseq

Issue - State: closed - Opened by wangjiawen2013 over 3 years ago - 1 comment

#200 - Number of regions

Issue - State: closed - Opened by wangjiawen2013 over 3 years ago - 3 comments

GitHub / databio/pepatac issues and pull requests