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
#508 - Rethink concordance filtering
Pull Request -
State: closed - Opened by MattWellie 8 months ago
#507 - Omit samples_cn field from gatksv final MT
Pull Request -
State: closed - Opened by cassimons 8 months ago
- 1 comment
#506 - Omit samples field for GATKSV callsets
Pull Request -
State: closed - Opened by cassimons 8 months ago
#505 - Add STRVCTVRE to GATK-SV pipeline
Issue -
State: closed - Opened by MattWellie 8 months ago
#504 - Minimal typo & RSID correction
Pull Request -
State: closed - Opened by MattWellie 8 months ago
- 1 comment
#503 - Typo correction in GATK-SV
Pull Request -
State: closed - Opened by MattWellie 8 months ago
- 1 comment
#502 - svType typo
Pull Request -
State: closed - Opened by cassimons 8 months ago
#501 - SeqrSV - variant DB links (gnomAD, Iranome) links incorrect
Issue -
State: closed - Opened by MattWellie 8 months ago
- 1 comment
#500 - Bugs in memory specification for Java jobs
Issue -
State: open - Opened by jmarshall 8 months ago
- 1 comment
#499 - Set thread count to core count
Pull Request -
State: closed - Opened by cassimons 8 months ago
- 2 comments
#498 - Large Cohort Tests Failing
Issue -
State: closed - Opened by vivbak 8 months ago
#497 - Add GCS specific implementation for exists
Pull Request -
State: closed - Opened by illusional 8 months ago
#496 - Update get_batch import to cpg-utils
Pull Request -
State: closed - Opened by illusional 8 months ago
- 3 comments
#495 - Further reduce dragmap threads
Pull Request -
State: closed - Opened by cassimons 8 months ago
- 1 comment
#494 - Set dragmap threads to nthreads -1
Pull Request -
State: closed - Opened by cassimons 9 months ago
#493 - Scrap early metamist registrations
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 4 comments
#492 - AIP tweaks, Stage wrapper arg to allow-missing outputs
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 3 comments
#491 - Pass specific dataset ID for the checkpoints
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#490 - Get AIP running on multiple datasets
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#489 - AIP config is sourced too soon
Issue -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#488 - Update SNV es-index analysis meta with seqr data type
Pull Request -
State: closed - Opened by EddieLF 9 months ago
- 1 comment
#487 - Fix docker workflow
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 2 comments
#486 - VEP schema decoding is causing silent failures
Issue -
State: open - Opened by MattWellie 9 months ago
#485 - ES Secrets for test
Issue -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#484 - AIP as pipeline stages
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#483 - Fix logs
Pull Request -
State: closed - Opened by vivbak 9 months ago
#482 - Check if Hap.py is working
Issue -
State: open - Opened by MattWellie 9 months ago
#481 - VEP 110
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 4 comments
#480 - Add xpos & co. in sv loader
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#479 - Pin cpg-workflows to older driver image
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 2 comments
#478 - Add globals values to SV MT
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 3 comments
#477 - New version pointing to wrong batch instance?
Issue -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#476 - Bump version: 1.15.3 → 1.16.0
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#475 - Create Template Configs & Update docs to reflect changes
Issue -
State: open - Opened by vivbak 10 months ago
#474 - Completes GATK-SV workflow
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#473 - Increase STRipy job CPUs to 4
Pull Request -
State: closed - Opened by EddieLF 10 months ago
#463 - gCNV merge + annotate
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 4 comments
#458 - Label Cromwell Jobs with relevant dataset
Issue -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#455 - Evaluate Hail +ve Annotation process
Issue -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#445 - Test align job
Pull Request -
State: closed - Opened by daniaki 10 months ago
- 2 comments
#443 - Canot generate annotated VCF output
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#442 - Updated submodule reference
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 3 comments
#439 - Test multiqc
Pull Request -
State: open - Opened by michael-harper 11 months ago
#438 - Test happy
Pull Request -
State: open - Opened by vivbak 11 months ago
- 2 comments
#432 - Test somalier
Pull Request -
State: closed - Opened by michael-harper 11 months ago
#429 - Create test_samtools.py
Pull Request -
State: closed - Opened by michael-harper 11 months ago
- 1 comment
#428 - Test fastqc
Pull Request -
State: closed - Opened by violetbrina 11 months ago
- 1 comment
#427 - Picard Tests
Pull Request -
State: closed - Opened by violetbrina 11 months ago
- 3 comments
#423 - Fixes to get things running with Analysis runner.
Pull Request -
State: closed - Opened by cassimons 12 months ago
- 3 comments
#419 - Add genotype job tests
Pull Request -
State: open - Opened by vivbak 12 months ago
#415 - STAR align stage
Pull Request -
State: closed - Opened by mgeaghan 12 months ago
#413 - Rare disease RNAseq workflow - trim stage
Pull Request -
State: closed - Opened by mgeaghan 12 months ago
- 1 comment
#409 - Adopt FilterGenotypes from gatk-sv upstream
Issue -
State: closed - Opened by MattWellie 12 months ago
Labels: enhancement
#405 - GATK-SV sample finder script
Pull Request -
State: closed - Opened by MattWellie 12 months ago
- 1 comment
#386 - Startup times are wild
Issue -
State: closed - Opened by MattWellie about 1 year ago
- 2 comments
#364 - enforce specific default python image
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#363 - Fragment workflows final workflow
Pull Request -
State: open - Opened by MattWellie about 1 year ago
#362 - Check that first_ and last_stages are always forced
Issue -
State: open - Opened by MattWellie about 1 year ago
#361 - Enable user-provided sample cohorts/datasets
Issue -
State: open - Opened by MattWellie about 1 year ago
- 5 comments
#360 - Fragment workflows
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
- 4 comments
#359 - Missed wdl outputs
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#358 - add a new stage to the seqr_loader
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#357 - complete revert
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#356 - GATK-SV re-jigging
Issue -
State: open - Opened by MattWellie about 1 year ago
#355 - Revert seqr loader changes
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#354 - Use current GitHub Action versions and set test timeout
Pull Request -
State: closed - Opened by jmarshall about 1 year ago
#353 - Add analysis record for AnnotateDataset job.
Pull Request -
State: closed - Opened by cassimons about 1 year ago
#352 - Investigating test/test_seqr_loader_dry.py unit test
Pull Request -
State: closed - Opened by jmarshall about 1 year ago
- 4 comments
#351 - Skip size check on hail outputs when creatting analysis records.
Pull Request -
State: closed - Opened by cassimons about 1 year ago
#350 - Edit for table-key consistency
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#349 - Fix test/test_large_cohort.py unit test
Pull Request -
State: closed - Opened by jmarshall about 1 year ago
- 4 comments
#348 - Switch to cpg_utils.slack implementation
Pull Request -
State: closed - Opened by lgruen about 1 year ago
#347 - Fix Annotation Bug
Pull Request -
State: closed - Opened by MattWellie about 1 year ago
#346 - Add rough WDL -> hail batch convert for GCNV
Pull Request -
State: open - Opened by illusional over 1 year ago
#345 - GATK-SV e2e implementation
Pull Request -
State: closed - Opened by MattWellie over 1 year ago
- 1 comment
#344 - Fix issue where ht is overwriting previous ht
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#343 - Add external IDs to PCA, if option supplied by user
Issue -
State: open - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#342 - Add subpopulation labels to PCA
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#341 - corrected storage request
Pull Request -
State: closed - Opened by MattWellie over 1 year ago
#340 - Move conifg commands to more universal location
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#339 - Rename extra_config in the CRAM MultiQC Stage
Issue -
State: open - Opened by KatalinaBobowik over 1 year ago
- 2 comments
#338 - Include option for more descriptive metadata when plotting ancestry PCA
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
#337 - Fix ordering of config files generated by large cohort pipeline
Issue -
State: open - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#336 - Expose the scatter_count parameter when genotyping
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#335 - Enable overwriting for DenseSubset stage
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
- 2 comments
#334 - Expose reference fasta as a configurable parameter for samtools stats
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#333 - Expose assume_sorted as a configurable Picard parameter
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#332 - Expose NumPCs as a configurable VerifyBamID parameter
Issue -
State: closed - Opened by KatalinaBobowik over 1 year ago
- 1 comment
#331 - Expose parameters
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#330 - Overwrite dense_subset.mt if it exists and force_stages is true
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#329 - Update sites table for HGDP-1kG
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#328 - Run PCA at DenseSubset stage
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#327 - Determine the set of sites to use for contamination detection with VerifyBamID
Issue -
State: open - Opened by KatalinaBobowik over 1 year ago
- 4 comments
#326 - Make configureable sites table be pulled from config
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#325 - Add PCA label
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#324 - complete artifactory paths for SV images
Pull Request -
State: closed - Opened by MattWellie over 1 year ago
#323 - Overwrite Outputs
Pull Request -
State: closed - Opened by vivbak over 1 year ago
- 2 comments
#322 - Rerun ancestry pca
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#321 - Remove colour palette which breaks AncestryPlots stage
Pull Request -
State: closed - Opened by KatalinaBobowik over 1 year ago
#320 - GATK-SV Fixes
Pull Request -
State: closed - Opened by vivbak over 1 year ago