Bishop-Laboratory RLPipes issues

Bishop-Laboratory / RLPipes

RLPipes: A standardized R-loop-mapping pipeline.

https://anaconda.org/bioconda/rlpipes

MIT License

3 stars 1 forks source link

issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

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

#93 CicadaDennis opened 5 months ago
2
install issue, possibly caused by genomeinfodbdata update ?

#92 joshtburdick closed 1 year ago
9
Need pinned dependencies for rule envs

#91 millerh1 closed 2 years ago
1
latency error

#90 markdunning closed 2 years ago
4
locked directory when trying to resume pipeline

#89 markdunning closed 2 years ago
4
No report output

#88 LeoColmet-Daage closed 2 years ago
3
v0.9.1 (bug fixes)

#87 millerh1 closed 2 years ago
2
Update devel

#86 millerh1 closed 2 years ago
0
Set default as macs2 and prefetch

#85 millerh1 closed 2 years ago
0
Location of downloaded genomes

#84 markdunning opened 2 years ago
1
Run RLPipe on user provided data

#83 pradyumnasagar closed 2 years ago
0
ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

#82 millerh1 closed 2 years ago
1
Error building test_data

#81 markdunning closed 2 years ago
6
Provide direct download option for getting public datasets

#80 millerh1 closed 2 years ago
2
Implement workaround for plant genomes

#79 millerh1 opened 2 years ago
0
fastp bug -- downgrade to v0.22.0

#77 millerh1 closed 2 years ago
1
Gzipped fastq files do not work

#76 millerh1 closed 2 years ago
0
CondaEnvException: Pip failed

#75 millerh1 closed 2 years ago
0
Format: "png" not recognized

#74 millerh1 closed 2 years ago
1
sh: 1: dot: not found

#73 millerh1 closed 2 years ago
1
FastX takes a very long time to index for read length calc

#72 millerh1 closed 2 years ago
0
Need rules for spikein data

#71 millerh1 opened 2 years ago
4
Automatic alignment to rDNA and telomere regions

#70 millerh1 opened 2 years ago
0
Create LICENSE

#69 millerh1 closed 2 years ago
0
Need `--no-report` flag for running pipeline just for peaks or coverage

#68 millerh1 closed 2 years ago
1
Split report data and report HTML generation rules

#67 millerh1 closed 2 years ago
1
Run Black and lint PEP8 in Pycharm

#66 millerh1 closed 2 years ago
1
Need bam, fastq, and public inputs passing tests

#65 millerh1 closed 3 years ago
0
Need pytest-click setup and working along with automated test data from AWS

#64 millerh1 closed 3 years ago
0
Need Click CLI implementation for argument parsing

#63 millerh1 closed 3 years ago
0
Need to supply PE check to MACS & need to ensure masc2/3 runs with correct flag

#62 millerh1 closed 3 years ago
0
Cleanup cli

#61 millerh1 closed 3 years ago
0
Need cleanup for checking .failed files and notifying user

#60 millerh1 opened 3 years ago
0
Need strand assignment of bams with coverage and callpeak rules

#59 millerh1 opened 3 years ago
0
Pipeline rewrite

#58 millerh1 closed 3 years ago
0
Research needed on rDNA / rep element alignment

#78 millerh1 opened 3 years ago
0
Need rule for FRiP analysis

#57 millerh1 opened 3 years ago
0
Needs rule for compiled report containing all samples in the run

#56 millerh1 opened 3 years ago
0
Need to connect R package: Substitute render function for reportion with R package implementation

#55 millerh1 closed 3 years ago
0
Peak annotation should be done with input peaks if available

#54 millerh1 closed 3 years ago
1
Needs rule for annotating peaks with gene symbols

#53 millerh1 closed 3 years ago
1
Technical IDR rule

#52 millerh1 closed 3 years ago
1
Needs blacklist beds for peak calling and coverage rules

#51 millerh1 opened 3 years ago
0
Needs macs2 called without input regardless of whether input is available. This is for QC reasons...

#50 millerh1 closed 3 years ago
0
Needs remove epic2 peak calling

#49 millerh1 closed 3 years ago
0
Needs macs3 rule and conda yaml

#48 millerh1 closed 3 years ago
0
Needs deepTools plotFingerprint rule

#47 millerh1 closed 3 years ago
0
Pipeline rewrite

#46 millerh1 closed 3 years ago
0
Needs shuffled DRIP-Seq bam file for testing

#45 millerh1 closed 3 years ago
0
Needs paired-end bam files for testing

#44 millerh1 closed 3 years ago
0