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
#308 - Adjust somalier.py to use the storage_for_cram_qc_job() function
Issue -
State: open - Opened by katiedelange 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
#305 - CRAM reference should be saved with the analysis object
Issue -
State: open - Opened by illusional over 1 year ago
#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