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Bishop-Laboratory
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RLPipes
RLPipes: A standardized R-loop-mapping pipeline.
https://anaconda.org/bioconda/rlpipes
MIT License
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md5sum mismatch when building rlseq conda environment, and after fixing build, subsequent errors in the rlseq environment
#93
CicadaDennis
opened
6 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
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