Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / populationgenomics/production-pipelines issues and pull requests

#319 - Explicitly skip VQSR Stages

Pull Request - State: closed - Opened by vivbak over 1 year ago

#318 - Skip stages

Pull Request - State: closed - Opened by vivbak over 1 year ago

#317 - quick fix version

Pull Request - State: closed - Opened by vivbak over 1 year ago

#316 - update prophecy toml

Pull Request - State: closed - Opened by vivbak over 1 year ago

#315 - Samples logged into Meta

Issue - State: open - Opened by vivbak over 1 year ago

#314 - annotate script and runner

Pull Request - State: closed - Opened by MattWellie over 1 year ago

#313 - Update stages to run PCA

Pull Request - State: closed - Opened by KatalinaBobowik over 1 year ago

#312 - Test commit 03a375f

Pull Request - State: closed - Opened by vivbak over 1 year ago

#311 - Display workflow

Pull Request - State: open - Opened by violetbrina over 1 year ago

#310 - Mitochondrial SNV pipeline PR 2 of N

Pull Request - State: open - Opened by cassimons over 1 year ago

#309 - Mitochondrial SNV pipeline PR 1 of N

Pull Request - State: open - Opened by cassimons over 1 year ago

#307 - Debugging Locally Docs

Pull Request - State: open - Opened by vivbak over 1 year ago

#306 - Fix-analysis-dataset

Pull Request - State: closed - Opened by violetbrina over 1 year ago - 1 comment

#304 - Add UTRAnnotator to VEP

Issue - State: open - Opened by MattWellie over 1 year ago - 2 comments

#303 - Concat threads

Pull Request - State: closed - Opened by cassimons over 1 year ago

#302 - Fix mito reff sync

Pull Request - State: closed - Opened by cassimons over 1 year ago

#301 - Remove sklearn

Pull Request - State: closed - Opened by vivbak over 1 year ago

#300 - Sync Broad mito reff data

Pull Request - State: closed - Opened by cassimons over 1 year ago

#299 - Mito copy script

Pull Request - State: closed - Opened by MattWellie over 1 year ago

#298 - Fix path to log file

Pull Request - State: closed - Opened by cassimons over 1 year ago

#297 - Handle unknown sex in stripy

Pull Request - State: closed - Opened by cassimons over 1 year ago

#296 - List outlier loci in stripy analysis record.

Pull Request - State: closed - Opened by cassimons over 1 year ago

#295 - Revert analysis_keys on CramQC

Pull Request - State: closed - Opened by vivbak over 1 year ago

#294 - CramQC stage can not run on exomes

Issue - State: open - Opened by cassimons over 1 year ago - 2 comments

#293 - Fix force re-run

Pull Request - State: closed - Opened by vivbak over 1 year ago

#292 - Forced re-run not working?

Issue - State: open - Opened by vivbak over 1 year ago - 1 comment
Labels: bug

#291 - Dataset stage reporting correct dataset

Pull Request - State: closed - Opened by illusional over 1 year ago - 1 comment

#290 - SampleQC -> DenseSubset for hgdp & 1KG.

Pull Request - State: closed - Opened by vivbak over 1 year ago

#289 - Fix path for tabix output file

Pull Request - State: closed - Opened by cassimons over 1 year ago

#288 - Use bcftools concat for gathering vcfs

Pull Request - State: closed - Opened by cassimons over 1 year ago

#287 - VCF merging strikes again

Issue - State: open - Opened by cassimons over 1 year ago
Labels: bug

#286 - Fix MakeSitesOnly Job

Pull Request - State: closed - Opened by vivbak over 1 year ago - 2 comments

#285 - Ensure a dependency between siteonly vcf generation and gather step

Pull Request - State: closed - Opened by illusional over 1 year ago

#284 - Fix MakeSitesOnlyVcf

Pull Request - State: closed - Opened by vivbak over 1 year ago

#283 - Somalier extract jobs producing empty output

Issue - State: open - Opened by cassimons over 1 year ago - 4 comments
Labels: bug

#282 - Joint genotyping: MakeSitesOnlyVcf jobs failing in seqr load pipeline.

Issue - State: closed - Opened by cassimons over 1 year ago - 7 comments

#281 - Fix the setting of pool labels

Pull Request - State: closed - Opened by lgruen over 1 year ago

#280 - Remove version bump from `cpg_workflows/defaults.toml`

Pull Request - State: closed - Opened by lgruen over 1 year ago

#279 - Skip hgdp samples

Pull Request - State: closed - Opened by vivbak over 1 year ago

#278 - Skip missing 1KG samples

Pull Request - State: closed - Opened by vivbak over 1 year ago

#277 - Remove frequencies (for now)

Pull Request - State: closed - Opened by vivbak over 1 year ago

#276 - Update relatedness param + improve docs

Pull Request - State: closed - Opened by vivbak over 1 year ago

#275 - Update TOMLS, Improve docs.

Pull Request - State: closed - Opened by vivbak over 1 year ago

#274 - Revert "Add vds only stage"

Pull Request - State: closed - Opened by vivbak over 1 year ago

#270 - Specify background datasets for PCA analysis

Pull Request - State: closed - Opened by vladsavelyev over 1 year ago

#220 - Add larcoh readme

Pull Request - State: open - Opened by KatalinaBobowik almost 2 years ago

#206 - Add script to fix alt contig MD5 sums in CRAM header

Pull Request - State: open - Opened by vladsavelyev almost 2 years ago - 3 comments

#201 - Abstract workflow state, add `JsonFileStateProvider`

Pull Request - State: open - Opened by vladsavelyev almost 2 years ago - 1 comment

#123 - GATK-SV: Add TrainGCNV stage

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago

#64 - More storage for the "Merge BAMs" job

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#61 - Use labelled pool, update batch job attrs/stats

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#58 - Wrappers for bioinformatics data types

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#57 - Support multiple sequencing types

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 2 comments

#56 - Update DRAGMAP image to use 1.3.0

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#27 - Fix ped

Pull Request - State: closed - Opened by vivbak over 2 years ago

#26 - Update get ped

Pull Request - State: closed - Opened by vivbak over 2 years ago

#25 - Get ped from sm

Pull Request - State: closed - Opened by vivbak over 2 years ago

#17 - Add docker sync

Pull Request - State: closed - Opened by vivbak over 2 years ago

#16 - Docker sync

Pull Request - State: closed - Opened by vivbak over 2 years ago - 1 comment

#2 - SVs production pipeline

Pull Request - State: closed - Opened by illusional almost 3 years ago

#1 - Commit rough germline CNV caller

Pull Request - State: closed - Opened by illusional about 3 years ago