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CCBR
/
RENEE
A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
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RSEQC version on biowulf has been updated
#120
slsevilla
closed
7 months ago
8
Error called in RSEM, TIN, BAM2BW: python 3.12 missing from user path
#119
slsevilla
closed
7 months ago
17
Add QC check if no reads are left after `cutadapt`
#118
slsevilla
opened
9 months ago
2
RNA Report is failing with too few samples.
#117
slsevilla
opened
9 months ago
2
STAR command is not using TMP dir - moving and removing files created in the outputdir
#116
slsevilla
opened
9 months ago
0
test: show that sif images are cached correctly
#115
kelly-sovacool
closed
9 months ago
0
test: setup basic cli tests with pytest
#114
kelly-sovacool
closed
9 months ago
4
SIF images not being copied from shared cache dir
#113
kelly-sovacool
closed
9 months ago
3
Feature request: Add "annoFuse"
#112
kopardev
opened
9 months ago
1
Feature Request: Add "STAR-Fusion"
#111
kopardev
opened
9 months ago
0
fix: run renee even if snakemake/singularity not in path
#110
kelly-sovacool
closed
9 months ago
0
Add HS1/T2T as genome reference
#109
slsevilla
closed
2 weeks ago
3
CONFIG.JSON does not allow for re-run of pipeline with altered sample list
#108
slsevilla
closed
9 months ago
7
Version not printed
#107
kopardev
closed
9 months ago
4
Renee build: qualimapinfo errors
#106
slsevilla
closed
1 month ago
2
fix: update RNA script to handle small or low diversity projects
#105
slsevilla
closed
10 months ago
1
RNA Report fails if there aren't 3 PCA's detected
#104
slsevilla
closed
10 months ago
0
docs: add badges
#103
kelly-sovacool
closed
10 months ago
0
chore: prepare release v2.5.11
#102
github-actions[bot]
closed
10 months ago
0
Rule fastq_screen error: No reference genomes were configured
#101
slsevilla
closed
10 months ago
2
style: run pre-commit on all files
#100
kelly-sovacool
closed
10 months ago
0
fix spelling errors
#99
kelly-sovacool
closed
10 months ago
0
fix: set default tmp dir for biowulf & frce
#98
kelly-sovacool
closed
10 months ago
2
support multiple versions on docs website
#97
kelly-sovacool
closed
3 months ago
1
ci: use semi-automated release & post-release actions
#96
kelly-sovacool
closed
10 months ago
1
release 2.5.11
#95
slsevilla
closed
10 months ago
5
Refactor the renee python package and move the GUI here
#94
kelly-sovacool
closed
3 months ago
14
ci: only run labels action when issue is opened
#93
kelly-sovacool
closed
10 months ago
0
ci: fix dryrun & lint github action
#92
kelly-sovacool
closed
10 months ago
0
Permissions fix, rNA report updates
#91
slsevilla
closed
10 months ago
1
Support Arriba for other genomes
#90
kelly-sovacool
opened
10 months ago
3
Migrate all resources to S3 bucket
#89
kelly-sovacool
opened
10 months ago
0
Feature/iss 81
#88
slsevilla
closed
10 months ago
0
fix: use genome json files in repo, not shared resources dir
#87
kelly-sovacool
closed
10 months ago
0
Create citation file
#86
kelly-sovacool
closed
10 months ago
3
fix: genome resource paths on FRCE
#85
kelly-sovacool
closed
10 months ago
0
error in rule `stats` on FRCE: can't open rRNA interval list
#84
kelly-sovacool
closed
10 months ago
0
error in RSEM: can't find resource file
#83
slsevilla
closed
10 months ago
10
error in RNA report on test data: cannot open the connection
#82
slsevilla
closed
10 months ago
8
error in star2p: could not create output file
#81
kelly-sovacool
closed
10 months ago
2
rNA report VOOM error with test data
#80
kopardev
closed
10 months ago
5
set default --tmp-dir depending on HPC platform
#79
kelly-sovacool
closed
10 months ago
5
feat: set fastq screen & kraken db shared resource paths depending on HPC
#78
kelly-sovacool
closed
10 months ago
2
chore: add pre-commit hook to validate JSON files
#77
kelly-sovacool
closed
10 months ago
0
chore: update changelog with note for v2.5.10
#76
kelly-sovacool
closed
10 months ago
0
add pre-commit hook to validate JSON files
#75
kelly-sovacool
closed
10 months ago
0
bugfix: adding missing commas; updating VERSION
#74
kopardev
closed
10 months ago
1
CI: fix dryrun action
#73
kelly-sovacool
closed
10 months ago
1
`cluster.json` bug in v2.5.9
#72
kopardev
closed
10 months ago
1
ci: delete sync-fork action
#71
kelly-sovacool
closed
10 months ago
1
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