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 5 months ago

#602 - 586 Multiallelic splitting

Pull Request - State: open - Opened by MattWellie 6 months ago

#600 - Allow workflow outputs to be written to `-analysis`

Pull Request - State: closed - Opened by MattWellie 6 months ago - 2 comments

#598 - GATK-SV samples go missing during the pipeline

Issue - State: open - Opened by MattWellie 6 months ago - 2 comments

#597 - Correct formatter arg in JoinRawCalls Stage

Pull Request - State: closed - Opened by MattWellie 6 months ago

#596 - Remove Metrics if run_metrics == False

Pull Request - State: closed - Opened by MattWellie 6 months ago

#595 - Don't run metrics sub-workflow, don't expect metrics outputs

Pull Request - State: closed - Opened by MattWellie 6 months ago

#594 - Split joint call multiallelics

Pull Request - State: closed - Opened by MattWellie 6 months ago

#593 - Fraser

Pull Request - State: open - Opened by mgeaghan 6 months ago

#592 - Allow indirect resource overrides of WDL sub-workflows

Pull Request - State: closed - Opened by MattWellie 6 months ago

#591 - Allow main builds to main artifactory

Pull Request - State: closed - Opened by MattWellie 6 months ago

#590 - Remove build-during-pr workflow

Pull Request - State: closed - Opened by MattWellie 6 months ago - 1 comment

#589 - gCNV bugfix - make variant IDs unique

Pull Request - State: closed - Opened by MattWellie 6 months ago - 2 comments

#588 - Add permanent sites table

Pull Request - State: closed - Opened by KatalinaBobowik 6 months ago - 2 comments

#587 - Insert T-Shirt job sizing for Cromwell and config overrides

Pull Request - State: closed - Opened by MattWellie 6 months ago - 2 comments

#586 - Split Multiallelic Variants in main pipeline

Issue - State: open - Opened by MattWellie 6 months ago

#585 - Metamist timeouts killing pipelines

Issue - State: open - Opened by MattWellie 6 months ago - 4 comments

#584 - BCFTools and BATCH_TMPDIR

Issue - State: open - Opened by MattWellie 6 months ago

#583 - Fix source of input data for GATK-SV stage

Pull Request - State: closed - Opened by MattWellie 6 months ago - 1 comment

#582 - Outrider side branch

Pull Request - State: closed - Opened by MattWellie 6 months ago

#581 - Make GATK-SV overrides reactive

Issue - State: closed - Opened by MattWellie 6 months ago

#580 - Unused argument not mandatory in workflow

Pull Request - State: closed - Opened by MattWellie 6 months ago

#579 - Ped fix 578

Pull Request - State: closed - Opened by MattWellie 6 months ago - 1 comment

#578 - GATK-SV rejects some valid Family IDs

Issue - State: closed - Opened by MattWellie 6 months ago

#577 - Inline python is bad

Pull Request - State: closed - Opened by MattWellie 6 months ago

#576 - Cheeky resource bumps

Pull Request - State: closed - Opened by MattWellie 6 months ago

#575 - Detection of PCR+/- is total Nonsense

Issue - State: open - Opened by MattWellie 6 months ago

#574 - Might need more resources by default in GATK-SV

Issue - State: closed - Opened by MattWellie 7 months ago

#573 - Update StrVCTVRE memory

Pull Request - State: closed - Opened by MattWellie 7 months ago - 1 comment

#572 - Allow various EvidenceQC overrides

Pull Request - State: closed - Opened by MattWellie 7 months ago

#571 - Adding config file for review

Pull Request - State: closed - Opened by michael-harper 7 months ago - 1 comment

#570 - Annotate sex fix

Pull Request - State: closed - Opened by MattWellie 7 months ago - 1 comment

#569 - Update default parameters for the rare disease rna seq pipeline

Pull Request - State: closed - Opened by mgeaghan 7 months ago - 1 comment

#568 - Inline python is hideous

Issue - State: open - Opened by MattWellie 7 months ago

#568 - Inline python is hideous

Issue - State: closed - Opened by MattWellie 7 months ago

#567 - Interval syntax simplification

Pull Request - State: closed - Opened by MattWellie 7 months ago

#567 - Interval syntax simplification

Pull Request - State: closed - Opened by MattWellie 7 months ago

#566 - Prevent old sample runs

Pull Request - State: closed - Opened by MattWellie 7 months ago

#565 - SampleQC Stage breaking during annotate_sex()

Pull Request - State: closed - Opened by michael-harper 7 months ago - 1 comment

#564 - Bump Scramble part 1 RAM

Pull Request - State: closed - Opened by MattWellie 7 months ago

#563 - gCNV sub-pr 1

Pull Request - State: closed - Opened by MattWellie 7 months ago

#562 - gCNV sub-pr 2

Pull Request - State: closed - Opened by MattWellie 7 months ago

#561 - gCNV sub-pr 3

Pull Request - State: closed - Opened by MattWellie 7 months ago

#560 - gCNV sub-pr 4

Pull Request - State: closed - Opened by MattWellie 7 months ago

#559 - gCNV sub-pr 5

Pull Request - State: closed - Opened by MattWellie 7 months ago

#558 - gCNV sub-pr 6

Pull Request - State: closed - Opened by MattWellie 7 months ago

#557 - A couple of suggestions

Pull Request - State: closed - Opened by MattWellie 7 months ago - 2 comments

#556 - Extend minimum status polling interval

Pull Request - State: closed - Opened by MattWellie 7 months ago

#555 - Simplify Genotype.expected_outputs() GVCF path construction

Pull Request - State: closed - Opened by jmarshall 7 months ago

#554 - Rare disease RNA pipeline - Outrider

Pull Request - State: closed - Opened by mgeaghan 7 months ago - 3 comments

#553 - force_stages argument isn't effective

Issue - State: open - Opened by MattWellie 7 months ago

#552 - Simplify Align.expected_outputs() CRAM path construction

Pull Request - State: closed - Opened by jmarshall 7 months ago - 1 comment

#551 - Rare disease RNA pipeline - count reads

Pull Request - State: closed - Opened by mgeaghan 7 months ago

#550 - Rare disease RNA pipeline - trim and align

Pull Request - State: closed - Opened by mgeaghan 7 months ago

#549 - Alter max polling interval for Cromwell

Pull Request - State: closed - Opened by MattWellie 7 months ago - 1 comment

#548 - Reheader crams sg id fix

Pull Request - State: open - Opened by EddieLF 7 months ago

#547 - Dataproc uses latest cpg-utils

Pull Request - State: closed - Opened by MattWellie 7 months ago - 2 comments

#546 - Update gnomad_methods submodule

Pull Request - State: closed - Opened by jmarshall 7 months ago

#545 - Fix cpg-utils dependency

Pull Request - State: closed - Opened by MattWellie 7 months ago

#544 - Add StrVCTVRE

Pull Request - State: closed - Opened by MattWellie 7 months ago

#542 - Ensure populated CramPaths have both path and index_path

Pull Request - State: closed - Opened by jmarshall 7 months ago - 3 comments

#541 - Cromwell job wrapper doesn't take access level any more

Pull Request - State: closed - Opened by MattWellie 7 months ago

#540 - Update default gatksv dockers

Pull Request - State: closed - Opened by MattWellie 7 months ago

#539 - Update to latest GATK-SV

Pull Request - State: closed - Opened by MattWellie 7 months ago

#538 - Use cpg utils get batch 2

Pull Request - State: closed - Opened by MattWellie 7 months ago - 1 comment

#537 - Handle existing outputs, for stage re-use

Pull Request - State: closed - Opened by vivbak 7 months ago - 1 comment

#536 - Add kinship>0.1 threshold for reporting Somalier ped issues to Slack

Pull Request - State: closed - Opened by EddieLF 7 months ago - 4 comments

#534 - Remove default dataproc init script

Pull Request - State: closed - Opened by illusional 8 months ago - 3 comments

#533 - Incorporate sample hash into multiQC input file

Pull Request - State: closed - Opened by MattWellie 8 months ago - 2 comments

#531 - Keep all GATK-SV sub-batch results

Pull Request - State: closed - Opened by MattWellie 8 months ago

#530 - Tweak AIP job names

Pull Request - State: closed - Opened by MattWellie 8 months ago

#529 - SVs in AIP

Pull Request - State: closed - Opened by MattWellie 8 months ago

#528 - Add dataset path to predetermined_qc_variants

Pull Request - State: closed - Opened by KatalinaBobowik 8 months ago - 2 comments

#527 - Use federated identities to auth to GCP

Pull Request - State: closed - Opened by illusional 8 months ago - 1 comment

#526 - Updated script for adjusting `@SQ` headers in existing CRAM files

Pull Request - State: closed - Opened by jmarshall 8 months ago - 6 comments

#525 - Add mandatory scatter_count parameter

Pull Request - State: closed - Opened by KatalinaBobowik 8 months ago

#524 - Update kinship threshold

Pull Request - State: closed - Opened by KatalinaBobowik 8 months ago

#523 - Update default variant sites table

Pull Request - State: closed - Opened by KatalinaBobowik 8 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 8 months ago - 1 comment

#521 - Reduce Metamist logging

Pull Request - State: closed - Opened by MattWellie 8 months ago - 1 comment

#520 - GATK-SV/Hail/Dataproc

Issue - State: closed - Opened by MattWellie 8 months ago - 1 comment

#519 - Allow ES-Index name registration without file checks

Pull Request - State: closed - Opened by MattWellie 8 months ago

#518 - Correct bug, repartition table

Pull Request - State: closed - Opened by MattWellie 8 months ago

#517 - Cache GCS exists redux: implementation

Pull Request - State: closed - Opened by MattWellie 8 months ago - 2 comments

#516 - Dataproc leads to misleading software executions

Issue - State: closed - Opened by MattWellie 8 months ago - 2 comments

#515 - Cache GCS exists 2; iterdir boogaloo

Pull Request - State: closed - Opened by MattWellie 8 months ago - 1 comment

#514 - Remove Dataproc in RD pipeline where possible

Pull Request - State: closed - Opened by MattWellie 8 months ago - 4 comments

#513 - Vep and ar-guid fixes

Pull Request - State: closed - Opened by MattWellie 8 months ago - 2 comments

#512 - Corrects ar_guid -> ar-guid

Pull Request - State: closed - Opened by MattWellie 8 months ago

#511 - Script to find SGs needing SV calling

Pull Request - State: closed - Opened by MattWellie 8 months ago

#510 - Update gnomad methods

Pull Request - State: closed - Opened by vivbak 8 months ago - 1 comment

#509 - Add config for machine type used for alignment.

Pull Request - State: closed - Opened by cassimons 8 months ago