Bishop-Laboratory/RLPipes issues and pull requests

#93 - md5sum mismatch when building rlseq conda environment, and after fixing build, subsequent errors in the rlseq environment

Issue - State: open - Opened by CicadaDennis 7 months ago - 2 comments

#92 - install issue, possibly caused by genomeinfodbdata update ?

Issue - State: closed - Opened by joshtburdick about 2 years ago - 9 comments

#91 - Need pinned dependencies for rule envs

Issue - State: closed - Opened by millerh1 over 2 years ago - 1 comment
Labels: enhancement

#90 - latency error

Issue - State: closed - Opened by markdunning over 2 years ago - 4 comments

#89 - locked directory when trying to resume pipeline

Issue - State: closed - Opened by markdunning over 2 years ago - 4 comments

#88 - No report output

Issue - State: closed - Opened by LeoColmet-Daage over 2 years ago - 3 comments
Labels: documentation, enhancement

#87 - v0.9.1 (bug fixes)

Pull Request - State: closed - Opened by millerh1 over 2 years ago - 2 comments

#86 - Update devel

Pull Request - State: closed - Opened by millerh1 over 2 years ago

#85 - Set default as macs2 and prefetch

Issue - State: closed - Opened by millerh1 over 2 years ago
Labels: enhancement

#84 - Location of downloaded genomes

Issue - State: open - Opened by markdunning over 2 years ago - 1 comment
Labels: enhancement

#83 - Run RLPipe on user provided data

Issue - State: closed - Opened by pradyumnasagar over 2 years ago

#82 - ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Issue - State: closed - Opened by millerh1 over 2 years ago - 1 comment
Labels: bug

#81 - Error building test_data

Issue - State: closed - Opened by markdunning over 2 years ago - 6 comments
Labels: bug

#80 - Provide direct download option for getting public datasets

Issue - State: closed - Opened by millerh1 almost 3 years ago - 2 comments
Labels: enhancement

#79 - Implement workaround for plant genomes

Issue - State: open - Opened by millerh1 almost 3 years ago
Labels: enhancement

#78 - Research needed on rDNA / rep element alignment

Issue - State: open - Opened by millerh1 about 3 years ago

#77 - fastp bug -- downgrade to v0.22.0

Issue - State: closed - Opened by millerh1 almost 3 years ago - 1 comment
Labels: bug

#76 - Gzipped fastq files do not work

Issue - State: closed - Opened by millerh1 almost 3 years ago
Labels: bug

#75 - CondaEnvException: Pip failed

Issue - State: closed - Opened by millerh1 almost 3 years ago
Labels: bug

#74 - Format: "png" not recognized

Issue - State: closed - Opened by millerh1 almost 3 years ago - 1 comment
Labels: bug

#73 - sh: 1: dot: not found

Issue - State: closed - Opened by millerh1 almost 3 years ago - 1 comment
Labels: bug

#72 - FastX takes a very long time to index for read length calc

Issue - State: closed - Opened by millerh1 almost 3 years ago
Labels: bug

#71 - Need rules for spikein data

Issue - State: open - Opened by millerh1 almost 3 years ago - 4 comments
Labels: enhancement

#70 - Automatic alignment to rDNA and telomere regions

Issue - State: open - Opened by millerh1 almost 3 years ago
Labels: enhancement

#69 - Create LICENSE

Pull Request - State: closed - Opened by millerh1 about 3 years ago

#68 - Need `--no-report` flag for running pipeline just for peaks or coverage

Issue - State: closed - Opened by millerh1 about 3 years ago - 1 comment
Labels: v0.9.0

#67 - Split report data and report HTML generation rules

Issue - State: closed - Opened by millerh1 about 3 years ago - 1 comment
Labels: enhancement

#66 - Run Black and lint PEP8 in Pycharm

Issue - State: closed - Opened by millerh1 about 3 years ago - 1 comment
Labels: v0.9.0

#65 - Need bam, fastq, and public inputs passing tests

Issue - State: closed - Opened by millerh1 about 3 years ago

#64 - Need pytest-click setup and working along with automated test data from AWS

Issue - State: closed - Opened by millerh1 about 3 years ago
Labels: v0.9.0

#63 - Need Click CLI implementation for argument parsing

Issue - State: closed - Opened by millerh1 about 3 years ago
Labels: v0.9.0

#62 - Need to supply PE check to MACS & need to ensure masc2/3 runs with correct flag

Issue - State: closed - Opened by millerh1 about 3 years ago
Labels: v0.9.0

#61 - Cleanup cli

Pull Request - State: closed - Opened by millerh1 about 3 years ago

#60 - Need cleanup for checking .failed files and notifying user

Issue - State: open - Opened by millerh1 about 3 years ago
Labels: enhancement

#59 - Need strand assignment of bams with coverage and callpeak rules

Issue - State: open - Opened by millerh1 about 3 years ago
Labels: enhancement

#58 - Pipeline rewrite

Pull Request - State: closed - Opened by millerh1 about 3 years ago

#57 - Need rule for FRiP analysis

Issue - State: open - Opened by millerh1 over 3 years ago
Labels: enhancement

#56 - Needs rule for compiled report containing all samples in the run

Issue - State: open - Opened by millerh1 over 3 years ago
Labels: enhancement

#55 - Need to connect R package: Substitute render function for reportion with R package implementation

Issue - State: closed - Opened by millerh1 over 3 years ago

#54 - Peak annotation should be done with input peaks if available

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#53 - Needs rule for annotating peaks with gene symbols

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#52 - Technical IDR rule

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#51 - Needs blacklist beds for peak calling and coverage rules

Issue - State: open - Opened by millerh1 over 3 years ago
Labels: enhancement

#50 - Needs macs2 called without input regardless of whether input is available. This is for QC reasons...

Issue - State: closed - Opened by millerh1 over 3 years ago

#49 - Needs remove epic2 peak calling

Issue - State: closed - Opened by millerh1 over 3 years ago

#48 - Needs macs3 rule and conda yaml

Issue - State: closed - Opened by millerh1 over 3 years ago

#47 - Needs deepTools plotFingerprint rule

Issue - State: closed - Opened by millerh1 over 3 years ago

#46 - Pipeline rewrite

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#45 - Needs shuffled DRIP-Seq bam file for testing

Issue - State: closed - Opened by millerh1 over 3 years ago

#44 - Needs paired-end bam files for testing

Issue - State: closed - Opened by millerh1 over 3 years ago

#43 - Needs total RNA-Seq bam files for testing

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#42 - Needs mm9 bam files for DRIP-Seq testing

Issue - State: closed - Opened by millerh1 over 3 years ago

#41 - Needs hg19 bam files for DRIP-Seq testing

Issue - State: closed - Opened by millerh1 over 3 years ago

#40 - Needs test bam files for R-ChIP and input

Issue - State: closed - Opened by millerh1 over 3 years ago

#39 - Needs test bam files for qDRIP-Seq and input

Issue - State: closed - Opened by millerh1 over 3 years ago

#38 - Needs test bam files for typical DRIP Seq and input

Issue - State: closed - Opened by millerh1 over 3 years ago

#37 - Refactor to make R-based functions a package that is loaded by the command-line scripts instead of part of the scripts

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#36 - Port the R input script to a robust command line framework in python

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#35 - See if you can break it from the perspective of user input

Issue - State: closed - Opened by millerh1 over 3 years ago

#33 - Needs a module that takes a set of peaks in GRanges format as input and annotates them

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#32 - Create the gh_pages branch and initialize documentation website

Issue - State: open - Opened by millerh1 over 3 years ago
Labels: documentation

#31 - Lacks documentation for correlation analysis along with usage information.

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#30 - Lacks tests for correlation analysis

Issue - State: closed - Opened by millerh1 over 3 years ago - 1 comment

#29 - Write the documentation

Issue - State: closed - Opened by millerh1 over 3 years ago

#28 - Develop the quality models

Issue - State: closed - Opened by millerh1 over 3 years ago

#27 - Conda build

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#26 - Refactor for install

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#25 - Add .circleci/config.yml

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#24 - Init ci

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#23 - Minor bug fix

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#22 - Need to test for GitHub workflows

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#21 - bwa-mem2 dependancy not found

Issue - State: closed - Opened by dmontemayor over 3 years ago - 1 comment
Labels: bug

#20 - Cannot find process_input.R file when parsing input

Issue - State: closed - Opened by dmontemayor over 3 years ago - 1 comment
Labels: bug

#19 - Development

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#18 - Configure tests

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#17 - Create RSeq - Copy

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#16 - Development

Pull Request - State: closed - Opened by millerh1 over 3 years ago

#15 - Write the manuscript

Issue - State: closed - Opened by millerh1 over 3 years ago

#14 - Update README.md

Pull Request - State: closed - Opened by millerh1 almost 4 years ago - 1 comment

#13 - Need for combined peak score in final_peaks.bed

Issue - State: closed - Opened by millerh1 almost 4 years ago - 1 comment
Labels: analysis, advanced, R

#12 - Finished module

Pull Request - State: closed - Opened by millerh1 almost 4 years ago

#10 - Updated RSeq script

Pull Request - State: closed - Opened by millerh1 almost 4 years ago

#9 - R-loop conservation analysis

Issue - State: closed - Opened by millerh1 almost 4 years ago - 1 comment
Labels: enhancement, analysis, intermediate

#8 - Snakemake refactor for multi-sample processing

Issue - State: closed - Opened by millerh1 almost 4 years ago
Labels: enhancement, advanced, Python

#7 - Support for bisDRIP/foot-printing/SMRF-Seq

Issue - State: open - Opened by millerh1 almost 4 years ago
Labels: enhancement

#6 - Sample binary classifier model R&D

Issue - State: closed - Opened by millerh1 almost 4 years ago
Labels: enhancement, research needed, analysis, beginner

#5 - Sample PASS/FAIL label assignment

Issue - State: closed - Opened by millerh1 almost 4 years ago
Labels: enhancement, research needed, analysis, advanced

#4 - Quality score model R&D

Issue - State: closed - Opened by millerh1 almost 4 years ago
Labels: enhancement, research needed, analysis, intermediate

#3 - Support for bigWig/Peak file input

Issue - State: closed - Opened by millerh1 almost 4 years ago - 1 comment
Labels: enhancement, intermediate, R, Python

#2 - remove extra files

Pull Request - State: closed - Opened by millerh1 about 4 years ago

#1 - hello world! dev branch

Pull Request - State: closed - Opened by millerh1 about 4 years ago

GitHub / Bishop-Laboratory/RLPipes issues and pull requests