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
#606 - Remove reference to inf_ploidy_using_var
Pull Request -
State: closed - Opened by michael-harper 8 months ago
#605 - Y-Ploidy Issues: Use variant data for X ploidy and ref-blocks for Y ploidy
Pull Request -
State: closed - Opened by michael-harper 8 months ago
#604 - Remove 'v' Prefix from VDS Version in Large Cohort Pipeline for Better Output Version Handling
Pull Request -
State: open - Opened by michael-harper 9 months ago
- 7 comments
#603 - Higher-level abstraction to replace `JobResource.get_java_mem_mb()`
Pull Request -
State: open - Opened by jmarshall 9 months ago
#602 - 586 Multiallelic splitting
Pull Request -
State: open - Opened by MattWellie 9 months ago
#601 - Fix Y Ploidy Inflation in SampleQC Stage: Allow variants_only_x_ploidy and variants_only_y_ploidy to be set in config file
Pull Request -
State: closed - Opened by michael-harper 9 months ago
- 1 comment
#600 - Allow workflow outputs to be written to `-analysis`
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 2 comments
#599 - Changing annotate_sex() to use reference blocks for ploidy calculationns in stead of variant sites in X and Y chromosomes
Pull Request -
State: closed - Opened by michael-harper 9 months ago
#598 - GATK-SV samples go missing during the pipeline
Issue -
State: open - Opened by MattWellie 9 months ago
- 2 comments
#597 - Correct formatter arg in JoinRawCalls Stage
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#596 - Remove Metrics if run_metrics == False
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#595 - Don't run metrics sub-workflow, don't expect metrics outputs
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#594 - Split joint call multiallelics
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#593 - Fraser
Pull Request -
State: open - Opened by mgeaghan 9 months ago
#592 - Allow indirect resource overrides of WDL sub-workflows
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#591 - Allow main builds to main artifactory
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#590 - Remove build-during-pr workflow
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#589 - gCNV bugfix - make variant IDs unique
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 2 comments
#588 - Add permanent sites table
Pull Request -
State: closed - Opened by KatalinaBobowik 9 months ago
- 2 comments
#587 - Insert T-Shirt job sizing for Cromwell and config overrides
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 2 comments
#586 - Split Multiallelic Variants in main pipeline
Issue -
State: open - Opened by MattWellie 9 months ago
#585 - Metamist timeouts killing pipelines
Issue -
State: open - Opened by MattWellie 9 months ago
- 4 comments
#584 - BCFTools and BATCH_TMPDIR
Issue -
State: open - Opened by MattWellie 9 months ago
#583 - Fix source of input data for GATK-SV stage
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#582 - Outrider side branch
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#581 - Make GATK-SV overrides reactive
Issue -
State: closed - Opened by MattWellie 9 months ago
#580 - Unused argument not mandatory in workflow
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#579 - Ped fix 578
Pull Request -
State: closed - Opened by MattWellie 9 months ago
- 1 comment
#578 - GATK-SV rejects some valid Family IDs
Issue -
State: closed - Opened by MattWellie 9 months ago
#577 - Inline python is bad
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#576 - Cheeky resource bumps
Pull Request -
State: closed - Opened by MattWellie 9 months ago
#575 - Detection of PCR+/- is total Nonsense
Issue -
State: open - Opened by MattWellie 9 months ago
#574 - Might need more resources by default in GATK-SV
Issue -
State: closed - Opened by MattWellie 10 months ago
#573 - Update StrVCTVRE memory
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#572 - Allow various EvidenceQC overrides
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#571 - Adding config file for review
Pull Request -
State: closed - Opened by michael-harper 10 months ago
- 1 comment
#570 - Annotate sex fix
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#569 - Update default parameters for the rare disease rna seq pipeline
Pull Request -
State: closed - Opened by mgeaghan 10 months ago
- 1 comment
#568 - Inline python is hideous
Issue -
State: open - Opened by MattWellie 10 months ago
#568 - Inline python is hideous
Issue -
State: closed - Opened by MattWellie 10 months ago
#567 - Interval syntax simplification
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#567 - Interval syntax simplification
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#566 - Prevent old sample runs
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#565 - SampleQC Stage breaking during annotate_sex()
Pull Request -
State: closed - Opened by michael-harper 10 months ago
- 1 comment
#564 - Bump Scramble part 1 RAM
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#563 - gCNV sub-pr 1
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#562 - gCNV sub-pr 2
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#561 - gCNV sub-pr 3
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#560 - gCNV sub-pr 4
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#559 - gCNV sub-pr 5
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#558 - gCNV sub-pr 6
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#557 - A couple of suggestions
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 2 comments
#556 - Extend minimum status polling interval
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#555 - Simplify Genotype.expected_outputs() GVCF path construction
Pull Request -
State: closed - Opened by jmarshall 10 months ago
#554 - Rare disease RNA pipeline - Outrider
Pull Request -
State: closed - Opened by mgeaghan 10 months ago
- 3 comments
#553 - force_stages argument isn't effective
Issue -
State: open - Opened by MattWellie 10 months ago
#552 - Simplify Align.expected_outputs() CRAM path construction
Pull Request -
State: closed - Opened by jmarshall 10 months ago
- 1 comment
#551 - Rare disease RNA pipeline - count reads
Pull Request -
State: closed - Opened by mgeaghan 10 months ago
#550 - Rare disease RNA pipeline - trim and align
Pull Request -
State: closed - Opened by mgeaghan 10 months ago
#549 - Alter max polling interval for Cromwell
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#548 - Reheader crams sg id fix
Pull Request -
State: open - Opened by EddieLF 10 months ago
#547 - Dataproc uses latest cpg-utils
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 2 comments
#546 - Update gnomad_methods submodule
Pull Request -
State: closed - Opened by jmarshall 10 months ago
#545 - Fix cpg-utils dependency
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#544 - Add StrVCTVRE
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#543 - Queuing STRipy stage jobs breaks for sequencing groups without Pathlike CRAM paths
Issue -
State: closed - Opened by EddieLF 10 months ago
Labels: bug
#542 - Ensure populated CramPaths have both path and index_path
Pull Request -
State: closed - Opened by jmarshall 10 months ago
- 3 comments
#541 - Cromwell job wrapper doesn't take access level any more
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#540 - Update default gatksv dockers
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#539 - Update to latest GATK-SV
Pull Request -
State: closed - Opened by MattWellie 10 months ago
#538 - Use cpg utils get batch 2
Pull Request -
State: closed - Opened by MattWellie 10 months ago
- 1 comment
#537 - Handle existing outputs, for stage re-use
Pull Request -
State: closed - Opened by vivbak 10 months ago
- 1 comment
#536 - Add kinship>0.1 threshold for reporting Somalier ped issues to Slack
Pull Request -
State: closed - Opened by EddieLF 10 months ago
- 4 comments
#535 - Improve (remove) hard path building, assume metamist as source of truth.
Pull Request -
State: closed - Opened by vivbak 10 months ago
#534 - Remove default dataproc init script
Pull Request -
State: closed - Opened by illusional 11 months ago
- 3 comments
#533 - Incorporate sample hash into multiQC input file
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 2 comments
#532 - Unexpected Cross-Batch Behavior in Hail Batch: Shared Sequencing Group IDs Between Batches Leading to Job Failures
Issue -
State: closed - Opened by michael-harper 11 months ago
- 2 comments
#531 - Keep all GATK-SV sub-batch results
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#530 - Tweak AIP job names
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#529 - SVs in AIP
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#528 - Add dataset path to predetermined_qc_variants
Pull Request -
State: closed - Opened by KatalinaBobowik 11 months ago
- 2 comments
#527 - Use federated identities to auth to GCP
Pull Request -
State: closed - Opened by illusional 11 months ago
- 1 comment
#526 - Updated script for adjusting `@SQ` headers in existing CRAM files
Pull Request -
State: closed - Opened by jmarshall 11 months ago
- 6 comments
#525 - Add mandatory scatter_count parameter
Pull Request -
State: closed - Opened by KatalinaBobowik 11 months ago
#524 - Update kinship threshold
Pull Request -
State: closed - Opened by KatalinaBobowik 11 months ago
#523 - Update default variant sites table
Pull Request -
State: closed - Opened by KatalinaBobowik 11 months ago
- 1 comment
#522 - Interim quick fix: Account for GB vs MiB in JobResource.get_java_mem_mb()
Pull Request -
State: closed - Opened by jmarshall 11 months ago
- 1 comment
#521 - Reduce Metamist logging
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 1 comment
#520 - GATK-SV/Hail/Dataproc
Issue -
State: closed - Opened by MattWellie 11 months ago
- 1 comment
#519 - Allow ES-Index name registration without file checks
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#518 - Correct bug, repartition table
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#517 - Cache GCS exists redux: implementation
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 2 comments
#516 - Dataproc leads to misleading software executions
Issue -
State: closed - Opened by MattWellie 11 months ago
- 2 comments
#515 - Cache GCS exists 2; iterdir boogaloo
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 1 comment
#514 - Remove Dataproc in RD pipeline where possible
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 4 comments
#513 - Vep and ar-guid fixes
Pull Request -
State: closed - Opened by MattWellie 11 months ago
- 2 comments
#512 - Corrects ar_guid -> ar-guid
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#511 - Script to find SGs needing SV calling
Pull Request -
State: closed - Opened by MattWellie 11 months ago
#510 - Update gnomad methods
Pull Request -
State: closed - Opened by vivbak 11 months ago
- 1 comment
#509 - Add config for machine type used for alignment.
Pull Request -
State: closed - Opened by cassimons 11 months ago