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populationgenomics
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production-pipelines
Genomics workflows for CPG using Hail Batch
MIT License
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Cohort analysis dataset name
#823
MattWellie
closed
2 months ago
0
Long-read correction
#822
MattWellie
closed
2 months ago
0
Long read SV correction
#821
MattWellie
closed
2 months ago
0
Update Hail pinning as we have deployed 0.2.132
#820
jmarshall
closed
2 months ago
0
Define a config parameter that keeps or removes samples that failed QC
#819
KatalinaBobowik
closed
2 months ago
0
Cleaner syntax for copying in MTs
#818
MattWellie
closed
2 months ago
0
Mt to es outside dataproc
#817
MattWellie
closed
2 months ago
2
Update VCF sample id for long reads
#816
MattWellie
closed
2 months ago
0
More flexibility in batch sizes
#815
MattWellie
closed
3 months ago
0
Src packaging
#814
MattWellie
opened
3 months ago
0
Move to `src/` layout?
#813
MattWellie
opened
3 months ago
0
GATK-SV transition to MultiCohorts
#812
MattWellie
closed
2 months ago
2
GATK-SV MultiCohort Transition
#811
MattWellie
closed
2 months ago
0
Talos updates
#810
MattWellie
closed
3 months ago
0
Allow for other reference genomes in bamtocram job
#809
EddieLF
closed
3 months ago
3
Clinvarbitration workflow
#808
MattWellie
closed
3 months ago
0
Add Ability to Remove Related Individuals from Background Dataset for PCA Analysis
#807
michael-harper
closed
2 months ago
1
Simplified VEP annotation
#806
MattWellie
closed
3 months ago
0
LR VCF query correction
#805
MattWellie
closed
3 months ago
0
Split Long-Read workflow
#804
MattWellie
closed
3 months ago
0
Use Talos endpoints
#803
MattWellie
closed
3 months ago
0
Simplify Alignment Job and Resolve SAM Flag Issue in CRAM to FASTQ Conversion
#802
michael-harper
opened
3 months ago
0
Annotate long read svs
#801
MattWellie
closed
3 months ago
0
Replace MtToEs stages Dataproc cluster usage with Hail Batch
#800
EddieLF
closed
2 months ago
6
Remove Pedigree as an argument
#799
MattWellie
closed
3 months ago
0
Localise the inputs, or cast as Strings
#798
MattWellie
closed
3 months ago
0
Run correction
#797
MattWellie
closed
3 months ago
0
Actually set the dependency
#796
MattWellie
closed
3 months ago
0
Talos TOML fix
#795
MattWellie
closed
3 months ago
0
Talos conversion
#794
MattWellie
closed
3 months ago
0
Handle Dataproc Jobs better
#793
MattWellie
opened
3 months ago
0
Improve Somalier Pedigree checking and Slack notifications
#792
EddieLF
opened
3 months ago
0
Manual dependency setting required for DataProc
#791
MattWellie
closed
1 month ago
1
Re-add dataproc depends_on
#790
MattWellie
closed
3 months ago
0
Add Functionality to Filter PCA Background Population in Large Cohort Pipeline Ancestry Stage
#789
michael-harper
closed
3 months ago
2
Genotypegvcfs mem gb config option
#788
EddieLF
closed
3 months ago
0
Fix GenotypeGVCFs HIGHMEM worker if-else option
#787
EddieLF
closed
3 months ago
0
Add HIGHMEM workers config option for GenotypeGVCFs jobs
#786
EddieLF
closed
3 months ago
0
Add resource override config option for genomics DB import memory
#785
EddieLF
closed
3 months ago
1
TASK: Robust Metamist Integrations
#784
milo-hyben
closed
1 month ago
1
Extract 'Alignment' and 'Genotype' to be separate independent pipelines
#783
michael-harper
opened
3 months ago
2
Target methods should be reviewed
#782
vivbak
opened
3 months ago
0
add_dataset is redundant in the Cohort Object
#781
vivbak
opened
4 months ago
0
Add --exclude-intervals h38 telomeres centromeres to genotypegvcfs jobs
#780
EddieLF
closed
3 months ago
3
Add test coverage
#779
milo-hyben
closed
1 month ago
1
Exome gCNV callsets should be clustered by family
#778
MattWellie
opened
4 months ago
0
Trim analysis callables
#777
MattWellie
opened
4 months ago
1
No datasets populated with Cohorts run
#776
vivbak
opened
4 months ago
0
RecursionError when submitting cpg_workflows pipeline runs
#775
vivbak
closed
2 months ago
1
remove "dataset =" from configs
#774
MattWellie
closed
4 months ago
0
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