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CCBR
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CHARLIE
Circrnas in Host And viRuses anaLysis pIpEline for Detection Annotation Quantification of circRNAs
https://ccbr.github.io/CHARLIE/
MIT License
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Support Altair Gridengine
#134
kelly-sovacool
opened
1 day ago
1
chore: 🤖 prepare release v0.11.1
#133
github-actions[bot]
closed
2 days ago
0
update docs for use with ccbrpipeliner/7
#132
kelly-sovacool
closed
5 days ago
0
star2p fails - cannot make directory
#131
kelly-sovacool
closed
5 days ago
3
fix: increase file latency wait
#130
kelly-sovacool
closed
1 week ago
0
fix: run python3 -E to make sure pythonpath is unset
#129
kelly-sovacool
closed
3 weeks ago
0
ciri failing even with 3 retries
#128
kelly-sovacool
closed
1 week ago
2
star1p slurm job failing even though rule succeeds
#127
kelly-sovacool
closed
1 week ago
0
concatenate reference files without using excessive memory
#126
kelly-sovacool
closed
3 weeks ago
0
fix: additional python paths in containers
#125
kelly-sovacool
closed
1 month ago
1
python path issue in create_circExplorer_merged_found_counts_table
#124
kelly-sovacool
closed
1 month ago
0
snakemake jobs failing due to missing output files which do exist
#123
kelly-sovacool
closed
1 week ago
16
do not concatenate reference files in RAM
#122
kelly-sovacool
closed
3 weeks ago
0
fix: reconfig needs to use platform-specific configfile
#121
kelly-sovacool
closed
1 month ago
0
clashing python libraries in singularity containers and ccbrpipeliner module
#120
kelly-sovacool
closed
1 month ago
3
fix: set singularity bind paths
#119
kelly-sovacool
closed
1 month ago
0
fix: don't check tempdir writeability
#118
kelly-sovacool
closed
1 month ago
0
TEMPDIR /lscratch/$SLURM_JOB_ID cannot be written to
#117
kelly-sovacool
closed
1 month ago
0
link to real testdata in tutorial & README
#116
kelly-sovacool
closed
5 days ago
0
chore: 🤖 prepare release v0.11.0
#115
github-actions[bot]
closed
2 months ago
0
update mkdocs
#114
kelly-sovacool
closed
2 months ago
0
refactor: setup bin/redirect to match other pipelines
#113
kelly-sovacool
closed
2 months ago
0
multiple versions of docs site
#112
kelly-sovacool
closed
2 months ago
0
refactor: use spooker & jobby from CCBR/Tools
#111
kelly-sovacool
closed
2 months ago
0
review docs website, update as needed for v0.11
#110
kelly-sovacool
opened
4 months ago
0
refactor CLI in python
#109
kelly-sovacool
opened
6 months ago
1
set singularity cachedir to workdir
#108
kelly-sovacool
closed
2 months ago
0
release v0.11.0 and add CHARLIE to ccbrpipeliner
#107
kopardev
closed
2 months ago
0
add option for different tmp-dir
#106
kelly-sovacool
closed
2 months ago
1
DCC has been deprecated in favor of `circtools detect`
#105
kelly-sovacool
opened
6 months ago
0
novoalign is not F/LOSS
#104
kelly-sovacool
closed
1 month ago
1
linter actions are failing
#103
kelly-sovacool
opened
8 months ago
0
create Docker containers and remove envmodules
#102
kelly-sovacool
closed
2 months ago
3
python 3.7 module is deprecated
#101
kelly-sovacool
closed
2 months ago
0
module missing
#100
kopardev
closed
7 months ago
1
convert to platform-agnostic pipeline
#99
kelly-sovacool
closed
2 months ago
15
update citation file with Zenodo DOI after we cut the next release
#98
kelly-sovacool
closed
2 months ago
1
chore: add precommit config files
#97
kelly-sovacool
closed
9 months ago
0
docs: create CITATION.cff
#96
kelly-sovacool
closed
10 months ago
0
Create CITATION.cff
#95
kelly-sovacool
closed
10 months ago
0
Create CHANGELOG
#94
kelly-sovacool
closed
2 months ago
0
V0.10.0 dev
#93
kopardev
closed
11 months ago
0
test
#92
kopardev
closed
2 months ago
0
Trimming dockerization
#91
kopardev
opened
1 year ago
0
SINGULARITY_CACHEDIR not working as expected.
#90
kopardev
closed
2 months ago
1
feature: add a toggle to use or not use singularity
#89
kopardev
closed
1 year ago
2
`circExplorer` calls fewer - strand circRNAs
#88
kopardev
closed
1 year ago
3
Issue85
#87
kopardev
closed
1 year ago
0
create all linear and all spliced BAMs
#86
kopardev
closed
1 year ago
0
label circRNAs has High Confidence Y/N
#85
kopardev
closed
1 year ago
1
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