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

#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

#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

#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