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Pull requests: populationgenomics/production-pipelines

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Pull requests list

Allow writing multiple files into a single analysis record
#1261 opened Jun 18, 2025 by EddieLF • Draft
1
Rename incompatible sampleqc fields
#1260 opened Jun 18, 2025 by joshuamschmidt Loading…
3
Reinstate 'sequencing_groups' job attributes
#1246 opened Jun 9, 2025 by jmarshall Loading…
1
Update image_path() invocations to include version arguments
#1204 opened May 5, 2025 by jmarshall Loading…
12
Fixing all paths
#1200 opened Apr 23, 2025 by michael-harper • Draft
1
Prepare Coverage Hail Table for Browser
#1185 opened Mar 31, 2025 by michael-harper Loading…
18
gnomAD Joint Freq/annotations into MT
#1166 opened Mar 24, 2025 by MattWellie Loading…
4
Update defaults for ICA pipeline
#1156 opened Mar 14, 2025 by Alexander-Stuckey Loading…
1
Avoid extracting absent SG from callset
#1150 opened Mar 4, 2025 by MattWellie Loading…
1
Lrs pipeline updates
#1115 opened Jan 17, 2025 by EddieLF • Draft
1
CPG flow division
#962 opened Oct 29, 2024 by violetbrina • Draft
@violetbrina
1
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…
3
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 htanudisastro 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
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…
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