CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline

https://CCBR.github.io/RENEE/

CCBR/RENEE Issues

RENEE build from .gtf
Updated in 21 hours
ResourceWarning in v2.6
Updated 6 days ago
error running jobby
Closed a month ago3
bug: snakemake issue in shared conda env on biowulf
Closed a month ago1
improve slurm complete/error email to describe where the pipeline output is
Updated 2 months ago
docs: FAQ on searching for failed jobs in log files
Closed a month ago2
docs: describe outputs
Closed a month ago
deprecate older genome versions after ~1 year, link to dockstore
Updated a month ago
feature: DTU - differential transcript usage
Updated 2 months ago
write output fastq validator to a log file instead of an output file
Updated 2 months ago
change fasta for hg19
Closed a month ago1
Feature request: RSEM outputs - counts matrix for isoforms
Closed a month ago5
Update docs (especially README) with list of supported genome versions
Closed 4 months ago
add --sif-cache flag to readme docs
Closed 4 months ago
`--help` functions report the name of the pipeline to be `__main__.py`
Closed 2 months ago2
Change human reference fasta
Closed a month ago3
set default human genome+annotation combo to match GDC
Closed a month ago3
add support for v45 reference from gencode
Closed 4 months ago3
consolidate build_cluster.json with cluster.json
Updated 4 months ago
snakemake/singularity loading error on main branch of 2.5.11-dev
Closed 6 months ago3
RSEQC version on biowulf has been updated
Closed 6 months ago8
Error called in RSEM, TIN, BAM2BW: python 3.12 missing from user path
Closed 6 months ago17
Add QC check if no reads are left after `cutadapt`
Updated 4 months ago1
RNA Report is failing with too few samples.
Updated 4 months ago
STAR command is not using TMP dir - moving and removing files created in the outputdir
Updated 2 months ago
SIF images not being copied from shared cache dir
Closed 7 months ago3
Feature request: Add "annoFuse"
Updated 4 months ago1
Feature Request: Add "STAR-Fusion"
Updated 4 months ago
Add HS1/T2T as genome reference
Updated 2 months ago2
CONFIG.JSON does not allow for re-run of pipeline with altered sample list
Closed 8 months ago7
Version not printed
Closed 8 months ago4
Renee build: qualimapinfo errors
Updated 4 months ago1
RNA Report fails if there aren't 3 PCA's detected
Closed 8 months ago
Rule fastq_screen error: No reference genomes were configured
Closed 8 months ago2
fix spelling errors
Closed 8 months ago
support multiple versions on docs website
Closed 2 months ago1
release 2.5.11
Closed 8 months ago5
Support Arriba for other genomes
Updated 4 months ago2
Migrate all resources to S3 bucket
Updated 4 months ago
error in rule `stats` on FRCE: can't open rRNA interval list
Closed 9 months ago
error in RSEM: can't find resource file
Closed 9 months ago10
error in RNA report on test data: cannot open the connection
Closed 9 months ago8
error in star2p: could not create output file
Closed 9 months ago2
rNA report VOOM error with test data
Closed 9 months ago5
set default --tmp-dir depending on HPC platform
Closed 8 months ago5
add pre-commit hook to validate JSON files
Closed 9 months ago
CI: fix dryrun action
Closed 8 months ago1
`cluster.json` bug in v2.5.9
Closed 9 months ago1
Large files are timing out for `bbmerge` and `kraken` rules
Closed 9 months ago
RENEE errors when attempting to deploy from git clone
Closed 8 months ago4