CHANGELOG.md

Changelog

2.2.1 (2024-07-26)

Bug Fixes

• also enlist ref for juno mapping (c6856d6)

2.2.0 (2024-07-25)

Features

• allow list as input type (254e1c8)

Bug Fixes

• fix typing (a135eb9)
• force tuple (46c3608)
• switch input_type to tuple (f406df2)

2.1.3 (2024-02-09)

Bug Fixes

• catch error if sample has multiple libraries (cff035a)
• error message (b66b9d5)
• parse illumina library correctly (2fd54a7)

2.1.2 (2024-01-25)

Bug Fixes

• restrict snakemake to v7 (393726c)

2.1.0 (2023-07-04)

Features

• add enlisting of bam and reference (4ef4be6)
• add vcf input files for mapping pipelines (cf98af3)
• include vcf in tests (cdcef21)

Bug Fixes

• correct vcf directory name (6512211)
• Fix juno_metadata not existing (9a478dd)
• fix unit test (ba8eee1)
• include vcf in checks (3e73986)

2.0.1 (2023-04-18)

Bug Fixes

• Make sure library also works in python 3.8 (fb9e7f6)

2.0.0 (2023-03-23)

⚠ BREAKING CHANGES

• Move snakemake args to dict

Features

• Add no-containers flag (9a5e33a)

Bug Fixes

• Make filepaths absolute (375c661)

Code Refactoring

• Move snakemake args to dict (afcd5d8)

Documentation

• Add docstrings to new functions (fec95b9)

Dependencies

• Update dependencies (74db4f5)

1.0.1 (2023-02-02)

Features

• Add py.typed (d49c3a6)

1.0.0 (2023-02-02)

⚠ BREAKING CHANGES

• Remove class abstraction in helper_functions

Features

• Add checks in github actions (ff6e986)
• Add mypy checking (754fe4d)
• Add release please (47e317b)
• Add run script (739d9d1)

Bug Fixes

• Add extra kwargs functionality to RunSnakemake (14ef3e7)
• Add kw_only=True for inheritance (c88f33c)
• Add openpyxl stubs to github action (6080082)
• Add RunSnakemake to init.py (a3b288b)
• Add type stubs to github action (2e0b2db)
• Change regex to string literal (c156c64)
• Fix github actions (9ec06fb)
• Fix library tests (64a5f2a)
• Fix main env and library_tests (0f21c89)
• Fix mypy checks (554c676)
• Fix previous commit (07e6d1f)
• Fix previous commit install (9299279)
• Fix setuptools versions in env (93f215a)
• Fix the main conda env (5eda41c)
• Fix unit tests for github actions (0009194)
• Fix up module structure (4c9adb1)
• Remove conda env in github action (3087ee4)
• Remove stuff from github action (9890d45)
• Update env location in github workflow (b6b8fec)
• Update mamba version (3686131)
• Use mamba in github action (247947b)

Code Refactoring

• Remove class abstraction in helper_functions (0f7b045)

Miscellaneous Chores

• release 1.0.0 (9c0b8fa)

1.0.0 (2023-02-01)

⚠ BREAKING CHANGES

• Remove class abstraction in helper_functions

Features

• Add checks in github actions (ff6e986)
• Add mypy checking (754fe4d)
• Add release please (47e317b)
• Add run script (739d9d1)

Bug Fixes

• Add extra kwargs functionality to RunSnakemake (14ef3e7)
• Add kw_only=True for inheritance (c88f33c)
• Add openpyxl stubs to github action (6080082)
• Add RunSnakemake to init.py (a3b288b)
• Add type stubs to github action (2e0b2db)
• Change regex to string literal (c156c64)
• Fix github actions (9ec06fb)
• Fix library tests (64a5f2a)
• Fix main env and library_tests (0f21c89)
• Fix mypy checks (554c676)
• Fix previous commit (07e6d1f)
• Fix previous commit install (9299279)
• Fix setuptools versions in env (93f215a)
• Fix the main conda env (5eda41c)
• Fix unit tests for github actions (0009194)
• Fix up module structure (4c9adb1)
• Remove conda env in github action (3087ee4)
• Remove stuff from github action (9890d45)
• Update env location in github workflow (b6b8fec)
• Update mamba version (3686131)
• Use mamba in github action (247947b)

Code Refactoring

• Remove class abstraction in helper_functions (0f7b045)