populationgenomics/cpg-utils issues and pull requests

#76 - Bump version: 4.6.2 → 4.6.3

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago

#75 - Add networkx for DAG, add `workflows/only_stages` parameter

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago

#74 - Bump version: 4.6.1 → 4.6.2: Don't set a pool label by default

Pull Request - State: closed - Opened by lgruen about 2 years ago

#73 - Support filtering samples by batch number

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago

#72 - Workflow: separate CramPath and BamPath classes, with explicit index_path

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago

#71 - Bump version: 4.6.0 → 4.6.1: Suppress debug output from google-auth

Pull Request - State: closed - Opened by lgruen about 2 years ago

#70 - Bump version: 4.5.4 → 4.6.0: Add get_google_identity_token method

Pull Request - State: closed - Opened by lgruen about 2 years ago

#69 - Use VEP 105 for RD

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago - 2 comments

#68 - VEP 104

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago - 3 comments

#67 - Bump version: 4.5.1 → 4.5.2: Fix packaging cpg_utils.workflows

Pull Request - State: closed - Opened by vladsavelyev about 2 years ago

#66 - Bump version: 4.5.1 → 4.5.2: Find all packages

Pull Request - State: closed - Opened by MattWellie about 2 years ago

#65 - Bump version: 4.5.0 → 4.5.1: Fix Python 3.8 compatibility with Dataproc

Pull Request - State: closed - Opened by lgruen about 2 years ago

#64 - Port the workflows library

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#63 - Bump version: 4.4.4 → 4.4.5

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#62 - Drop python 3.10 specific syntax for dataproc

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#61 - Add hap.py 0.3.15

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#60 - Bump version: 4.4.2 → 4.4.3: Revert to Python 3.8 compatible syntax for Dataproc

Pull Request - State: closed - Opened by lgruen over 2 years ago

#59 - Fix linting

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#58 - Bump version: 4.4.1 → 4.4.2

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#57 - Config template updates

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#56 - Add happy vcfeval to images

Pull Request - State: closed - Opened by MattWellie over 2 years ago

#55 - Bump version: 4.3.6 → 4.4.0: Corrected format string

Pull Request - State: closed - Opened by MattWellie over 2 years ago

#54 - upload pathing change

Pull Request - State: closed - Opened by MattWellie over 2 years ago - 1 comment

#53 - Allow absolute image paths in config

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#52 - Bump version: 4.3.4 → 4.3.5: Add `fail_gracefully` flag to `read_secret`

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#51 - Bump version: 4.3.3 → 4.3.4: Use driver image instead of deprecated sm-api image

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#50 - Bump version: 4.3.2 → 4.3.3: Validate config, include default toml into package

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#49 - Bump version: 4.3.1 → 4.3.2: add frozendict into reqs

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#48 - Bump version: 4.2.3 → 4.3.0: Support comma-separated list of configs

Pull Request - State: closed - Opened by lgruen over 2 years ago

#47 - Add Namespace enum

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#46 - Bump version: 4.3.0 → 4.3.1: Add config default `config-template.toml`, get references and images by key

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#45 - Bump version: 4.2.2 → 4.2.3: Use dict instead of MutableMapping

Pull Request - State: closed - Opened by lgruen over 2 years ago

#44 - Bump version: 4.2.1 → 4.2.2

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#43 - Fix mypy pre-commit toml error

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#42 - Update pre-commit hooks

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago - 1 comment

#41 - Bump version: 4.2.0 → 4.2.1: Fix imports

Pull Request - State: closed - Opened by lgruen over 2 years ago

#40 - Parametrise path scheme in `dataset_path`

Pull Request - State: closed - Opened by vladsavelyev over 2 years ago

#35 - Bump version: 4.1.3 → 4.2.0: Use a config file instead of environment variables

Pull Request - State: closed - Opened by lgruen over 2 years ago - 1 comment

#29 - Add get_group_members for supporting GCS access-group cache

Pull Request - State: closed - Opened by illusional over 2 years ago - 1 comment

#7 - Add sample-metadata foundations

Pull Request - State: closed - Opened by illusional over 3 years ago - 1 comment

GitHub / populationgenomics/cpg-utils issues and pull requests