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populationgenomics
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production-pipelines
Genomics workflows for CPG using Hail Batch
MIT License
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Clinvarbitration workflow
#808
MattWellie
closed
13 hours ago
0
Add Ability to Remove Related Individuals from Background Dataset for PCA Analysis
#807
michael-harper
opened
3 days ago
1
Simplified VEP annotation
#806
MattWellie
closed
8 hours ago
0
LR VCF query correction
#805
MattWellie
closed
5 days ago
0
Split Long-Read workflow
#804
MattWellie
closed
5 days ago
0
Use Talos endpoints
#803
MattWellie
opened
5 days ago
0
Simplify Alignment Job and Resolve SAM Flag Issue in CRAM to FASTQ Conversion
#802
michael-harper
opened
6 days ago
0
Annotate long read svs
#801
MattWellie
closed
6 days ago
0
Replace MtToEs stages Dataproc cluster usage with Hail Batch
#800
EddieLF
opened
1 week ago
0
Remove Pedigree as an argument
#799
MattWellie
closed
1 week ago
0
Localise the inputs, or cast as Strings
#798
MattWellie
closed
1 week ago
0
Run correction
#797
MattWellie
closed
1 week ago
0
Actually set the dependency
#796
MattWellie
closed
1 week ago
0
Talos TOML fix
#795
MattWellie
closed
1 week ago
0
Talos conversion
#794
MattWellie
closed
1 week ago
0
Handle Dataproc Jobs better
#793
MattWellie
opened
1 week ago
0
Improve Somalier Pedigree checking and Slack notifications
#792
EddieLF
opened
1 week ago
0
Manual dependency setting required for DataProc
#791
MattWellie
opened
1 week ago
1
Re-add dataproc depends_on
#790
MattWellie
closed
1 week ago
0
Add Functionality to Filter PCA Background Population in Large Cohort Pipeline Ancestry Stage
#789
michael-harper
closed
2 weeks ago
2
Genotypegvcfs mem gb config option
#788
EddieLF
closed
3 weeks ago
0
Fix GenotypeGVCFs HIGHMEM worker if-else option
#787
EddieLF
closed
3 weeks ago
0
Add HIGHMEM workers config option for GenotypeGVCFs jobs
#786
EddieLF
closed
3 weeks ago
0
Add resource override config option for genomics DB import memory
#785
EddieLF
closed
3 weeks ago
1
TASK: Robust Metamist Integrations
#784
milo-hyben
opened
3 weeks ago
1
Extract 'Alignment' and 'Genotype' to be separate independent pipelines
#783
michael-harper
opened
3 weeks ago
0
Target methods should be reviewed
#782
vivbak
opened
3 weeks ago
0
add_dataset is redundant in the Cohort Object
#781
vivbak
opened
3 weeks ago
0
Add --exclude-intervals h38 telomeres centromeres to genotypegvcfs jobs
#780
EddieLF
closed
3 weeks ago
3
Add test coverage
#779
milo-hyben
opened
4 weeks ago
1
Exome gCNV callsets should be clustered by family
#778
MattWellie
opened
1 month ago
0
Trim analysis callables
#777
MattWellie
opened
1 month ago
1
No datasets populated with Cohorts run
#776
vivbak
opened
1 month ago
0
RecursionError when submitting cpg_workflows pipeline runs
#775
vivbak
opened
1 month ago
0
remove "dataset =" from configs
#774
MattWellie
closed
1 month ago
0
Joint genotyping fixes
#773
EddieLF
closed
1 month ago
2
Simplify call to complete_analysis_job
#772
illusional
opened
1 month ago
0
Refactoring main for local dev
#771
milo-hyben
opened
1 month ago
2
No need to run gsutil inside the job
#770
MattWellie
closed
1 month ago
0
Bam2cram, corrected
#769
MattWellie
closed
1 month ago
1
Invalid Cohort IDs as inputs fails silently
#768
vivbak
opened
1 month ago
0
Pin Hail to the version deployed in CPG's installation
#767
jmarshall
closed
1 month ago
1
Pass index into xy removal
#766
MattWellie
closed
1 month ago
0
Castrate aneuploidies
#765
MattWellie
closed
1 month ago
0
:sparkles:MultiCohorts:sparkles:
#764
vivbak
closed
6 days ago
3
AnnotateCohort takes Spiced up output
#763
MattWellie
closed
1 month ago
0
Spiced Up ID analysis entries needs to be consistent
#762
MattWellie
closed
1 month ago
0
Move SV ID updates to post annotation
#761
MattWellie
closed
1 month ago
1
Fix escaping in stripy verbose
#760
cassimons
closed
1 month ago
0
Update stripy logging command
#759
EddieLF
closed
1 month ago
0
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