databio/pepatac issues and pull requests

#100 - Docs into dev

Pull Request - State: closed - Opened by vreuter over 5 years ago

#99 - missing links to log files

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment
Labels: docs

#98 - hg19_TSS.tgz is empty

Issue - State: closed - Opened by sthair over 5 years ago - 3 comments

#97 - bamsitestoWig

Issue - State: closed - Opened by nsheff over 5 years ago - 3 comments

#96 - bug in gzipping

Issue - State: closed - Opened by nsheff over 5 years ago - 2 comments
Labels: bug

#95 - samtools given bad options

Issue - State: closed - Opened by caldodge over 5 years ago - 8 comments

#94 - question about core use

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment
Labels: question

#93 - Create standalone R package

Issue - State: open - Opened by nsheff over 5 years ago - 3 comments
Labels: enhancement, question

#92 - geofetch tutorial is outdated

Issue - State: closed - Opened by nsheff over 5 years ago
Labels: docs

#91 - empty temp folders

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment

#90 - Default settings/ empty peak files

Issue - State: closed - Opened by sthair over 5 years ago - 8 comments

#89 - Release 0.8.6

Pull Request - State: closed - Opened by nsheff over 5 years ago

#88 - gzip

Issue - State: closed - Opened by nsheff over 5 years ago

#87 - MACS2 parameters customized in yaml

Issue - State: closed - Opened by shmilyfhh over 5 years ago - 4 comments

#86 - Improving efficiency in bigwig files with 0 counts

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment

#85 - unable to follow issue template

Issue - State: closed - Opened by stolarczyk over 5 years ago - 1 comment
Labels: priority-low

#84 - TypeError: '>' not supported between instances of 'list' and 'int'

Issue - State: closed - Opened by gcapture over 5 years ago - 8 comments

#83 - Release 0.8.5

Pull Request - State: closed - Opened by jpsmith5 over 5 years ago - 2 comments

#82 - repository size

Issue - State: closed - Opened by nsheff over 5 years ago - 2 comments

#81 - default issue

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment

#80 - TypeError: cannot concatenate 'str' and 'NoneType' objects

Issue - State: closed - Opened by shmilyfhh over 5 years ago - 5 comments
Labels: bug

#79 - Docs revisions

Pull Request - State: closed - Opened by nsheff almost 6 years ago

#78 - docs links in to tutorial leads to 404 errors

Issue - State: closed - Opened by nsheff almost 6 years ago - 2 comments
Labels: docs

#77 - Error when running "pipelines/pepatac.py"

Issue - State: closed - Opened by hiroyukikato911 almost 6 years ago - 10 comments

#76 - tutorial example question

Issue - State: closed - Opened by nsheff almost 6 years ago - 2 comments
Labels: docs

#75 - Change default deduplication tool and improve messaging

Pull Request - State: closed - Opened by jpsmith5 almost 6 years ago

#74 - add summarize dependencies to container

Issue - State: closed - Opened by nsheff almost 6 years ago - 6 comments

#73 - R function for BiocProject

Issue - State: closed - Opened by nsheff almost 6 years ago - 6 comments

#72 - fastqc reports to pypiper

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#71 - zip fastq files

Issue - State: closed - Opened by nsheff about 6 years ago - 2 comments
Labels: priority - high

#70 - Missing TSS instructions

Issue - State: closed - Opened by nsheff about 6 years ago - 3 comments

#69 - zcat on macos

Issue - State: closed - Opened by nsheff about 6 years ago - 2 comments

#68 - error messages when missing bamSitesToWig requirements

Issue - State: closed - Opened by nsheff about 6 years ago - 2 comments

#67 - config folder

Issue - State: closed - Opened by nsheff about 6 years ago

#66 - Getting started

Issue - State: closed - Opened by stolarczyk about 6 years ago - 2 comments

#65 - resources

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#64 - Hotfix 0.8.2

Pull Request - State: closed - Opened by jpsmith5 about 6 years ago

#63 - better genomes help message

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#62 - Hotfix 0.8.1

Pull Request - State: closed - Opened by jpsmith5 about 6 years ago

#61 - Release 0.8

Pull Request - State: closed - Opened by nsheff over 6 years ago

#60 - dedup count bug

Issue - State: closed - Opened by nsheff over 6 years ago - 2 comments

#59 - smoothed track on single end data

Issue - State: closed - Opened by nsheff over 6 years ago - 4 comments

#58 - streamline filenames

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment

#57 - samblaster

Issue - State: closed - Opened by nsheff over 6 years ago - 3 comments

#56 - demo results

Issue - State: closed - Opened by nsheff over 6 years ago - 11 comments

#55 - PEPATAC_summarizer.R fails with large inputs

Issue - State: closed - Opened by rcorces over 6 years ago - 7 comments
Labels: bug

#54 - Missing figures.tsv files for alignments_figs_summary.html

Issue - State: closed - Opened by rcorces over 6 years ago - 2 comments
Labels: question

#53 - more informative assembly missing error messages

Issue - State: closed - Opened by nsheff over 6 years ago - 3 comments
Labels: enhancement

#52 - Preemption issues again

Issue - State: closed - Opened by rcorces over 6 years ago - 4 comments

#51 - summary plots are incorrect for incomplete samples

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment

#50 - Exception: There is no bowtie2 index directory for hg38

Issue - State: closed - Opened by jf2016GH over 6 years ago - 11 comments

#49 - summarizer error

Issue - State: closed - Opened by nsheff over 6 years ago - 20 comments

#48 - Dev

Pull Request - State: closed - Opened by jpsmith5 over 6 years ago - 7 comments

#47 - container update

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment

#46 - check for genomes early

Issue - State: closed - Opened by nsheff over 6 years ago - 2 comments

#45 - readme needs list of prerequisites

Issue - State: closed - Opened by nsheff over 6 years ago - 2 comments

#44 - standardize summarizer ATAC_Looper_Summary_plot.R

Issue - State: closed - Opened by nsheff over 6 years ago - 10 comments
Labels: enhancement

#43 - dockerfile missing libmysqlclient

Issue - State: closed - Opened by nsheff over 6 years ago - 3 comments
Labels: bug

#42 - Pipeline does not catch improperly paired fastq files

Issue - State: closed - Opened by rcorces over 6 years ago - 4 comments
Labels: bug

#41 - occasional chrM reads

Issue - State: closed - Opened by rcorces over 6 years ago - 18 comments
Labels: bug, enhancement

#40 - dockerize

Issue - State: closed - Opened by nsheff over 6 years ago - 1 comment
Labels: enhancement

#39 - add all plots to summary output with report_figure

Issue - State: closed - Opened by nsheff over 6 years ago - 4 comments

#38 - Fix issues #36, #37

Pull Request - State: closed - Opened by jpsmith5 over 6 years ago - 4 comments

#37 - temp.bam file?

Issue - State: closed - Opened by rcorces over 6 years ago - 1 comment

#36 - "Aligned_Reads" - raw aligned reads vs non-duplicate aligned reads?

Issue - State: closed - Opened by rcorces almost 7 years ago - 1 comment
Labels: enhancement, question

#35 - Add --backup option

Issue - State: closed - Opened by rcorces almost 7 years ago - 6 comments
Labels: enhancement

#34 - pyTSSenrichment.py not handling interrupt signals properly

Issue - State: closed - Opened by rcorces almost 7 years ago - 16 comments

#33 - release v0.6

Pull Request - State: closed - Opened by nsheff almost 7 years ago - 1 comment

#32 - bam2bed_shift.pl functionality

Issue - State: closed - Opened by rcorces almost 7 years ago - 25 comments
Labels: question

#31 - Job with failed.flag still running

Issue - State: closed - Opened by rcorces almost 7 years ago - 7 comments

#30 - Inconsistent pipeline performance when disk space is exceeded

Issue - State: closed - Opened by rcorces almost 7 years ago - 9 comments
Labels: bug

#29 - Single end

Pull Request - State: closed - Opened by nsheff almost 7 years ago

#28 - new tool_path function incorrectly includes tool filename

Issue - State: closed - Opened by nsheff about 7 years ago - 1 comment

#27 - Odd behavior in re-initiated jobs

Issue - State: closed - Opened by rcorces about 7 years ago - 22 comments

#26 - Dev

Pull Request - State: closed - Opened by nsheff about 7 years ago

#25 - looper clean doesnt remove tmp files from alignments?

Issue - State: closed - Opened by rcorces about 7 years ago - 13 comments
Labels: bug

#24 - bedgraph (?) output in log file

Issue - State: closed - Opened by rcorces over 7 years ago - 1 comment
Labels: enhancement

#23 - Make skewer quiet?

Issue - State: closed - Opened by rcorces over 7 years ago - 1 comment
Labels: enhancement, question

#22 - Job preemption still not perfect

Issue - State: closed - Opened by rcorces over 7 years ago - 16 comments

#21 - Release 0.4

Pull Request - State: closed - Opened by nsheff over 7 years ago - 2 comments

#20 - Use PipelineManager.run's follow parameter to report peak count

Pull Request - State: closed - Opened by vreuter over 7 years ago - 1 comment

#19 - TSS enrichment failure doesn't halt the pipeline?

Issue - State: closed - Opened by vreuter over 7 years ago - 5 comments
Labels: question

#18 - Installation requirements

Issue - State: closed - Opened by vreuter over 7 years ago - 4 comments

#17 - F-Seq, trimmer choices, peak count

Pull Request - State: closed - Opened by vreuter over 7 years ago - 3 comments

#16 - fseq option for peak calling, and choice model for trimmer options

Pull Request - State: closed - Opened by vreuter over 7 years ago

#15 - Summary Plot script is currently limited to human alignments

Issue - State: closed - Opened by rcorces over 7 years ago - 21 comments
Labels: bug, question

#14 - README structure suggestion

Issue - State: closed - Opened by carbonwei over 7 years ago - 4 comments

#13 - Multiple read_type columns in looper summarize output

Issue - State: closed - Opened by rcorces over 7 years ago - 2 comments

#12 - Make bowtie2 parameterizable

Issue - State: closed - Opened by nsheff over 7 years ago - 9 comments
Labels: enhancement

#11 - Add option for abbreviated pipeline

Issue - State: closed - Opened by rcorces over 7 years ago - 11 comments

#10 - pull recent master changes into dev.

Pull Request - State: closed - Opened by nsheff over 7 years ago

#9 - Clarify usage of --prealignments

Issue - State: closed - Opened by rcorces over 7 years ago - 6 comments

#8 - TSS enrichment plot improvement

Issue - State: closed - Opened by carbonwei over 7 years ago - 7 comments

#7 - pre-looper usage tutorial of ATACseq pipeline

Issue - State: closed - Opened by carbonwei over 7 years ago - 11 comments

#6 - Feature proposals

Issue - State: closed - Opened by nsheff over 7 years ago - 4 comments

#5 - Version 0.3 release PR

Pull Request - State: closed - Opened by nsheff over 7 years ago

#4 - Add cutsToWig utility

Pull Request - State: closed - Opened by nsheff over 7 years ago

#3 - Add draft cut locator

Pull Request - State: closed - Opened by nsheff over 7 years ago

#2 - Development changes into master

Pull Request - State: closed - Opened by nsheff over 7 years ago

#1 - Fix line 374. replace + with comma

Pull Request - State: closed - Opened by rcorces almost 8 years ago - 3 comments

GitHub / databio/pepatac issues and pull requests