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uab-cgds-worthey
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quac
🦆 Quality Control of WGS and exome samples 🦆
https://quac.readthedocs.io
GNU General Public License v3.0
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adding testing detection function fix
#96
wilkb777
closed
2 months ago
0
Supplying list of files for external FASTQC causes pipeline to fail
#95
wilkb777
closed
2 months ago
0
Bump pymdown-extensions from 9.5 to 10.0 in /configs/mkdocs
#94
dependabot[bot]
closed
8 months ago
0
QuaC is published!!
#93
ManavalanG
closed
10 months ago
0
Bring master branch up to date on sample config as input and doc fixes
#92
ManavalanG
closed
11 months ago
0
Documentation update related to #85 and #86
#91
ManavalanG
closed
11 months ago
1
Provide sample filepaths via user-provided sample config file - Part 4 (allow sample renaming in multiqc)
#90
ManavalanG
closed
11 months ago
0
Provide sample filepaths via user-provided sample config file - Part 3 (priorQC mode)
#89
ManavalanG
closed
11 months ago
0
Provide sample filepaths via user-provided sample config file - Part 2 (exome minimal mode)
#88
ManavalanG
closed
11 months ago
0
Provide sample filepaths via user-provided sample config file - Part 1 (wgs minimal mode)
#87
ManavalanG
closed
11 months ago
0
Feature request: add support for specifying samples directly
#86
Redmar-van-den-Berg
closed
11 months ago
2
Please add documentation on how to set QC limits
#85
Redmar-van-den-Berg
closed
11 months ago
1
Minor updates
#84
ManavalanG
closed
1 year ago
0
Bring master branch up to date on doc fixes
#83
ManavalanG
closed
1 year ago
0
Improves documentation based on user feeback
#82
ManavalanG
closed
1 year ago
0
Bring master branch up to date
#81
ManavalanG
closed
1 year ago
0
Refactors to account for user's environment-specific SLURM setup
#80
ManavalanG
closed
1 year ago
4
System testing CI workflow gets triggered twice and one of them (tends to) fail
#79
ManavalanG
closed
1 year ago
7
Github actions for system testing failed with error "No space left on device"
#78
ManavalanG
closed
1 year ago
1
Have users try out QuaC in Slurm cluster which is not cheaha.
#77
ManavalanG
closed
1 year ago
0
CLI script not accounting for user's environment specific slurm args requirements
#76
ManavalanG
closed
1 year ago
1
Adds system testing workflow to github actions
#75
ManavalanG
closed
1 year ago
2
Make system testing github actions run faster
#74
ManavalanG
opened
1 year ago
3
Create sbatch args using cluster config file
#73
ManavalanG
closed
1 year ago
0
Check mount paths exist
#72
ManavalanG
closed
1 year ago
1
Verify singularity mount paths exist
#71
ManavalanG
closed
1 year ago
0
Swtich singularity+conda setup to singularity setup for snakemake tasks
#70
ManavalanG
closed
1 year ago
0
Removing use of conda env for tasks within snakemake pipeline
#69
ManavalanG
closed
1 year ago
6
--conda-create-envs-only results in errors - CreateCondaEnvironmentException and container creation failed
#68
ManavalanG
opened
1 year ago
6
Autocreate user-provided dirpath if they don't exist
#67
ManavalanG
closed
1 year ago
1
document environment variables
#66
brentp
opened
1 year ago
3
Create a script to retrieve necessary datasets for workflow configs
#65
ManavalanG
closed
1 year ago
0
Decouples github readme from readthedocs
#64
ManavalanG
closed
1 year ago
0
Add license and fix PR template bug
#63
ManavalanG
closed
1 year ago
0
Set readthedocs to use master branch
#62
ManavalanG
closed
1 year ago
0
Restructure docs and host using ReadTheDocs
#61
ManavalanG
closed
1 year ago
2
Rename default branch `master` to `main`
#60
ManavalanG
opened
1 year ago
0
More features to make quac generic to non-cheaha users
#59
ManavalanG
closed
1 year ago
3
Allow usage of custom slurm partitions
#58
ManavalanG
closed
1 year ago
0
Make snakemake's slurm job submission optional
#57
ManavalanG
closed
1 year ago
4
Use snakemake-minimal in conda env to reduce bloat
#56
ManavalanG
closed
1 year ago
3
Separate output directory option for per-sample QC results and Project-level QC results
#55
ManavalanG
opened
2 years ago
1
Update quac-watch config's median insert size threshold for WGS
#54
ManavalanG
closed
1 year ago
0
Remove git submodules
#53
ManavalanG
closed
1 year ago
2
Use container solution for covviz installation instead of conda
#52
ManavalanG
closed
1 year ago
3
Choose and add license
#51
ManavalanG
opened
2 years ago
0
Number of decimal digits to show in multiqc report
#50
ManavalanG
opened
2 years ago
0
Explicitly define conda environments
#49
ManavalanG
closed
1 year ago
4
Qualimap fails due to out of memory
#48
ManavalanG
closed
1 year ago
2
QuaC stalls at singularity+conda env creation step for multiqc
#47
ManavalanG
closed
1 year ago
17
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