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Pull requests: populationgenomics/production-pipelines

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Pull requests list

Manually override aneuploidies, Optimise output paths
#986 opened Nov 13, 2024 by MattWellie Loading…
2
Implement cohort name -> ID
#967 opened Nov 3, 2024 by MattWellie Loading…
2
CPG flow division
#962 opened Oct 29, 2024 by violetbrina • Draft
@violetbrina
1
Create alignment hash on first get, reuse thereafter
#958 opened Oct 27, 2024 by MattWellie Loading…
1
Cohort ID vs Cohort Name
#951 opened Oct 24, 2024 by vivbak Loading…
7
Ancestry no dp gcta testing
#915 opened Sep 26, 2024 by michael-harper • Draft
1
Add readgroup level stats config option for Picard metrics
#910 opened Sep 19, 2024 by EddieLF Loading…
1
Pip-Audit
#909 opened Sep 18, 2024 by nevoodoo Loading…
2
Testing PCA on GCTA
#908 opened Sep 18, 2024 by michael-harper • Draft
1
Fix cohort.get_sequencing_groups in cpg_workflows targets.py
#899 opened Sep 11, 2024 by EddieLF • Draft
2
Sandwich stage for BioHEART only
#898 opened Sep 10, 2024 by hopedisastro Loading…
@EddieLF
1
Remove Dataproc from AncestryPlots Stage
#897 opened Sep 9, 2024 by michael-harper • Draft
1
Replacing bazam + removing non-dragmap aligners
#871 opened Aug 4, 2024 by michael-harper Loading…
2
Relatedness, no Dataproc large cohort Change is exclusively within the scope of the large cohort pipeline
#870 opened Aug 2, 2024 by MattWellie Loading…
3
Removing options for biobambam as tool for marking duplicates core Changes to the cpg-workflows api enhancement New feature or request
#844 opened Jul 23, 2024 by michael-harper Loading…
2
Simplify Alignment Job and Resolve SAM Flag Issue in CRAM to FASTQ Conversion
#802 opened Jun 25, 2024 by michael-harper • Draft
Extract 'Alignment' and 'Genotype' to be separate independent pipelines
#783 opened Jun 5, 2024 by michael-harper Loading…
7
Refactoring main for local dev
#771 opened May 28, 2024 by milo-hyben • Draft
2
Enable pre-commit mypy checks to typecheck cpg_utils usage
#728 opened May 6, 2024 by jmarshall Loading…
2
Environment Lock
#693 opened Apr 17, 2024 by nevoodoo Loading…
1 task done
4
Sites table generation
#692 opened Apr 16, 2024 by michael-harper • Draft
1
Local Integration Test??
#671 opened Apr 4, 2024 by vivbak • Draft
Pca dataproc str
#667 opened Mar 27, 2024 by hopedisastro Loading…
Parallel exports gcloud compose [prototype]
#639 opened Mar 11, 2024 by MattWellie • Draft
3
Fix intermediate file overwriting in test-tmp bucket to prevent script failures due to existing files
#631 opened Feb 28, 2024 by michael-harper Loading…
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