Cpg-flow

Bug Fixes

- **Makefile**: Add uv to to init commands
([`44ac58d`](https://github.com/populationgenomics/cpg-flow/commit/44ac58d3c29e323b1ab0e94490c33293ef93b79a))

- **package.yaml,Makefile**: Make docs out of ci-build command
([`4df965b`](https://github.com/populationgenomics/cpg-flow/commit/4df965bf9e74594abc8cee4b7c5a2203319f4325))

- **package.yaml,Makefile**: Install uv, uv sync
([`5fcadd9`](https://github.com/populationgenomics/cpg-flow/commit/5fcadd9d9743993feeaffc4f77442d36da1d207e))

- **Makefile**: Add debug pwd/ls
([`282f62c`](https://github.com/populationgenomics/cpg-flow/commit/282f62c40223de18769f22f3fd470db57f5d01e7))

- **pyproject.toml,src/cpg_flow/metamist.py-,+5**: Merge alpha
([`84ef763`](https://github.com/populationgenomics/cpg-flow/commit/84ef7632eae5abab9c1ef2fa4b3ed6f423d22e85))

- **src/cpg_flow/workflow.py**: Fix url path
([`bb0e839`](https://github.com/populationgenomics/cpg-flow/commit/bb0e83949b9c1ff55d002bf884374897ae38d1d1))

- **src/cpg_flow/workflow.py**: Info log the url
([`def1d03`](https://github.com/populationgenomics/cpg-flow/commit/def1d031ee97aaf81cf2892c7267b839cf975c15))

- **src/cpg_flow/workflow.py**: Fix bucket/blob name
([`ebfe31a`](https://github.com/populationgenomics/cpg-flow/commit/ebfe31a2af795232cf512d690e0ebd0f061ce596))

- **src/cpg_flow/workflow.py**: Fix bug on 577 to use str
([`89ff6fe`](https://github.com/populationgenomics/cpg-flow/commit/89ff6fed88a83a237768252b2cac78a599fd463f))

- **src/cpg_flow/workflow.py**: Write_to_gcs_bucket convert to str
([`b782cfa`](https://github.com/populationgenomics/cpg-flow/commit/b782cfaf95cf9cc705cc631f85c86ffb87de9b9b))

- **src/cpg_flow/workflow.py**: Create write_to_gcs_bucket
([`0452eb8`](https://github.com/populationgenomics/cpg-flow/commit/0452eb8c588ff328d9dc3b2b41c31f41fa40a83b))

- **src/cpg_flow/workflow.py**: Fix plotly plot save
([`d3e70a6`](https://github.com/populationgenomics/cpg-flow/commit/d3e70a6a5cd33ffb22e1425a8e553f00a3e2b68a))

- **src/cpg_flow/workflow.py**: Don't fail on connection error
([`0348bd4`](https://github.com/populationgenomics/cpg-flow/commit/0348bd47236ca92973404413eaa036a1aacc0131))

- **src/cpg_flow/workflow.py**: Rm () from self.web_prefix
([`7d4f9b3`](https://github.com/populationgenomics/cpg-flow/commit/7d4f9b3e681c7c5fd9f8858d2b6cf2e4303c88ee))

- **src/cpg_flow/workflow.py**: Get_alignment_inputs_hash()
([`71ccd0c`](https://github.com/populationgenomics/cpg-flow/commit/71ccd0c9cb4daac23db6e4bc73af702fedabe3c9))

- **src/cpg_flow/workflow.py**: Use builtin web_prefix method
([`6362036`](https://github.com/populationgenomics/cpg-flow/commit/63620365bc71ab957d1cdd555bb62379d9ef5cba))

- **src/cpg_flow/,tests/**: Metamist custom cohort mock fixed
([`1bb0ddd`](https://github.com/populationgenomics/cpg-flow/commit/1bb0ddd6c6bfb67fbb7be8531c423b4610786c05))

- **src/cpg_flow/workflow.py**: Fix 'skipped' attr missing in nx graph
([`1c64e6b`](https://github.com/populationgenomics/cpg-flow/commit/1c64e6bdf7e680ed01c6fb844ff95a2caf098a40))

- **graph.py**: Rm search in repo for stages (removed in cpg_flow)
([`648e7d7`](https://github.com/populationgenomics/cpg-flow/commit/648e7d7b269c80150640abbd0fdc422e411e29cc))

- **multicohort**: Replace multicohort name with hash
([`7ce04bd`](https://github.com/populationgenomics/cpg-flow/commit/7ce04bda8ed4b0cd9efb3984679b3e8c15ee3770))

multicohort.name too long for *nix. hash will be static in length

- Replicate prod pipes PR1068
([`cf782c9`](https://github.com/populationgenomics/cpg-flow/commit/cf782c93686ec4346e3730af165a892986cf68fc))

- Migrate prod pipes PR951
([`7f16948`](https://github.com/populationgenomics/cpg-flow/commit/7f169485444438ae260ae10dbfea1c5d022c6b8a))

- **inputs.py,tests/test_multicohort.py**: Replicate prod pipes PR989
([`f1d6fcd`](https://github.com/populationgenomics/cpg-flow/commit/f1d6fcdbd6390c0d6eaa09ae72f589294f90e2ef))

- **defaults.toml**: Remove unnecessary options and add more comment
([`57f80ca`](https://github.com/populationgenomics/cpg-flow/commit/57f80ca6eb4e92efca56a751e5aea60bf5cc07c8))

Build System

- **pyproject.toml,uv.lock**: Add pre-commit as core dep
([`f03ecaf`](https://github.com/populationgenomics/cpg-flow/commit/f03ecafe99dd5d0042d6c58f27b0bfd26a71fc94))

Chores

- Update badges.yaml with test results and coverage
([`52aa984`](https://github.com/populationgenomics/cpg-flow/commit/52aa9841781820c5c43936f351cea678440e2209))

- Update badges.yaml with test results and coverage
([`1994f07`](https://github.com/populationgenomics/cpg-flow/commit/1994f07de95f0bdccaac68ff465130e3c0196df2))

- Update badges.yaml with test results and coverage
([`ba9fdb8`](https://github.com/populationgenomics/cpg-flow/commit/ba9fdb8b9125bf0bbafa9ee0955a6780b867118f))

- Update badges.yaml with test results and coverage
([`7f2b1ff`](https://github.com/populationgenomics/cpg-flow/commit/7f2b1ff4b8442936fe1c568aecc5832a59f086c3))

- Update badges.yaml with test results and coverage
([`0a93026`](https://github.com/populationgenomics/cpg-flow/commit/0a9302638ed75acfe2a0858516f2b8ca00d7c4f2))

- Update badges.yaml with test results and coverage
([`cd46929`](https://github.com/populationgenomics/cpg-flow/commit/cd46929ddda6de27010f3428625f23060d86b72c))

- Update badges.yaml with test results and coverage
([`9cfccdb`](https://github.com/populationgenomics/cpg-flow/commit/9cfccdbd8c5681b3a56a083aba61d130282f9422))

- Update badges.yaml with test results and coverage
([`d3664b4`](https://github.com/populationgenomics/cpg-flow/commit/d3664b4937b11dfd6f5bc216cf3d822a734d461a))

- Update badges.yaml with test results and coverage
([`28a23d6`](https://github.com/populationgenomics/cpg-flow/commit/28a23d682e92dbd259083b990a2a6fe6353b09f7))

- Update badges.yaml with test results and coverage
([`837d6ba`](https://github.com/populationgenomics/cpg-flow/commit/837d6ba911bc47b665a18e920d915417773039ac))

- Update badges.yaml with test results and coverage
([`189c60b`](https://github.com/populationgenomics/cpg-flow/commit/189c60bbdb48766dc6e491ead97bf36c300b3f55))

- Update badges.yaml with test results and coverage
([`28eac64`](https://github.com/populationgenomics/cpg-flow/commit/28eac6433c9f9d62bd99d9de7114d6f9a09be047))

- Update badges.yaml with test results and coverage
([`b0c3331`](https://github.com/populationgenomics/cpg-flow/commit/b0c333119e3c11a8a66e9ed66a81a64285fc48ea))

- Update badges.yaml with test results and coverage
([`54d505d`](https://github.com/populationgenomics/cpg-flow/commit/54d505d9a5bf174f934bfdee64886842842eb9ee))

- Update badges.yaml with test results and coverage
([`2deb20b`](https://github.com/populationgenomics/cpg-flow/commit/2deb20b5dc1e9ba8b9c5088ee8a3ecd9240166c7))

- Update badges.yaml with test results and coverage
([`5f70383`](https://github.com/populationgenomics/cpg-flow/commit/5f70383ede7d4b4232bd3ecc57966ca9f06795c3))

- Update badges.yaml with test results and coverage
([`1605c75`](https://github.com/populationgenomics/cpg-flow/commit/1605c7576efedd48741bc293ebde97d8719be366))

- Update badges.yaml with test results and coverage
([`5ee9b6d`](https://github.com/populationgenomics/cpg-flow/commit/5ee9b6dca33b1920a7c60e29da57d14bc8a1418c))

- Update badges.yaml with test results and coverage
([`bf48667`](https://github.com/populationgenomics/cpg-flow/commit/bf48667521560337747ac4d3bbe36d72bc47005b))

- Update badges.yaml with test results and coverage
([`e50ab94`](https://github.com/populationgenomics/cpg-flow/commit/e50ab94dce6059609e2deb8cb1bd56d0ca632b56))

- Update badges.yaml with test results and coverage
([`478d74a`](https://github.com/populationgenomics/cpg-flow/commit/478d74a0572b61875686c5130a66e513e5519a42))

- Update badges.yaml with test results and coverage
([`2174a17`](https://github.com/populationgenomics/cpg-flow/commit/2174a178b942609670fca46d2407d71d841d6254))

- Update badges.yaml with test results and coverage
([`5dad740`](https://github.com/populationgenomics/cpg-flow/commit/5dad740cebc6b84ce41e0eeb319d3bb33b51e02b))

Continuous Integration

- **package.yaml**: Continue on error build docs
([`4666ccb`](https://github.com/populationgenomics/cpg-flow/commit/4666ccb1b864e044091c345447d3a2d944de9182))

- **Makefile**: Add uv run to all docs commands
([`9d9bc00`](https://github.com/populationgenomics/cpg-flow/commit/9d9bc00e6c696c569ef120f6743b714699356061))

- **package.yaml**: Run on push to alpha, re-add if condition
([`8cdf8cf`](https://github.com/populationgenomics/cpg-flow/commit/8cdf8cf4445dfc092caffa5c7f245d7d0d143daf))

- **Makefile**: Fail make docs command to prevent relase
([`5f6f6bd`](https://github.com/populationgenomics/cpg-flow/commit/5f6f6bda2ded1e393626e835d86f9a401125e131))

- **package.yaml**: Run on PR to alpha
([`b7d54d1`](https://github.com/populationgenomics/cpg-flow/commit/b7d54d1e5f08e47cb322d8cbd62e24752e7cef27))

- **package.yaml**: Rm if for main/alpha
([`3e2a8b4`](https://github.com/populationgenomics/cpg-flow/commit/3e2a8b4e144db1ba47267b5a904970906cd4e5c6))

- **package.yaml**: Add package run on push to alpha to debug
([`248ab87`](https://github.com/populationgenomics/cpg-flow/commit/248ab8769f4f1f08a3dc5b238253c62cabfea030))

- **docker.yaml**: Echo out the docker tag
([`c991340`](https://github.com/populationgenomics/cpg-flow/commit/c991340339a58a9752fb74094d925474bcf40dd1))

- **update-badges.yaml**: Continue push on fail
([`d3fed1b`](https://github.com/populationgenomics/cpg-flow/commit/d3fed1b7266693a0ff6c2ae7d5b89681f4b77dd2))

- **test.yaml**: Fix removed code in test.yaml
([`f353a89`](https://github.com/populationgenomics/cpg-flow/commit/f353a89da5aeffe9584f3cc3256d5763838a07db))

- **update-badges.yaml,docs/badges.yaml**: Fix missing data for badges
([`21d4e0b`](https://github.com/populationgenomics/cpg-flow/commit/21d4e0be10101d7a6717d568e1630f0c5641eddd))

- **update-badges.yaml,docs/badges.yaml**: Success if no changes to branch
([`8122669`](https://github.com/populationgenomics/cpg-flow/commit/812266941988f5a556352d9bfaa27a46dc73dbaf))

- **update-badges.yaml,docs/badges.yaml**: Rm trailing whitespace
([`2e547c0`](https://github.com/populationgenomics/cpg-flow/commit/2e547c0903197169527c58d8cc09ea12f389c771))

- **update-badges.yaml**: Add token to checkout
([`2e5de8c`](https://github.com/populationgenomics/cpg-flow/commit/2e5de8caad7ee2727a4983ad26496c9a14425542))

- **test.yaml**: Cat badge data
([`3221492`](https://github.com/populationgenomics/cpg-flow/commit/322149295ce4c2b61e791e3e27ed9a6667ba6079))

- **update-badges.yaml**: Rm final push
([`a782609`](https://github.com/populationgenomics/cpg-flow/commit/a7826099c1ff877e8d4becbf1000f30645e27eaa))

- **update-badges.yaml**: Add git pull
([`cbca5c4`](https://github.com/populationgenomics/cpg-flow/commit/cbca5c4b6100473379a0e7d8d0ddb1b4d430a56f))

- **update-badges.yaml**: Fix push bug -m flag
([`ce05b2b`](https://github.com/populationgenomics/cpg-flow/commit/ce05b2b1d2e4d386196112e2525a8e3a7b0a9cd5))

- **update-badges.yaml**: Commit with ci bot
([`ff8561c`](https://github.com/populationgenomics/cpg-flow/commit/ff8561cbf7e19945d5d3e188a4a162cde1a117e6))

Documentation

- **targets/__init__.py**: Write docs for targets
([`bc6c0e8`](https://github.com/populationgenomics/cpg-flow/commit/bc6c0e8c66b815cde55c0f3183cfe5683c2a819c))

- **./,docs/**: Fix readme links
([`c4cda73`](https://github.com/populationgenomics/cpg-flow/commit/c4cda73d75ecb4489865c495ebda79fb9633d694))

- **./,docs/**: Update docs and readme urls
([`938658e`](https://github.com/populationgenomics/cpg-flow/commit/938658e1bd2ccf71cdfa22c8fe235267be599e16))

Features

- **src/cpg_flow/workflow.py**: Save graph to web bucket
([`9a47711`](https://github.com/populationgenomics/cpg-flow/commit/9a47711541e9a9d3aa89f325ada118da34ae7bb7))

- Migrate prod pipes PR311
([`4663cc2`](https://github.com/populationgenomics/cpg-flow/commit/4663cc20774e7a641dab775f5421976feb9b80ef))

Refactoring

- **utils.py,workflow.py**: Mv write_to_gcs_bucket to utils
([`950ba94`](https://github.com/populationgenomics/cpg-flow/commit/950ba94a2a8ea6c98450feca410683068c7720b0))

- **Tests**: Remove seqr.toml as it is not used or required
([`5f340b6`](https://github.com/populationgenomics/cpg-flow/commit/5f340b6141d99ce5546db9aef485dbd809e0c9d3))

- **.gitignore**: Add .scannerwork
([`649e4ac`](https://github.com/populationgenomics/cpg-flow/commit/649e4ac5f51378bbe039e523553be03c808a3a65))

Bug Fixes

- **.dummy**: Force release
([`15b8906`](https://github.com/populationgenomics/cpg-flow/commit/15b8906cbc07338f3ab730a365e89feeecbc4c7a))

Build System

- **pyproject.toml,uv.lock**: Update jinja2 to 3.1.5
([`4dbdf15`](https://github.com/populationgenomics/cpg-flow/commit/4dbdf15a031ee8cd010efb9884458670bfecdaaf))

- **uv.lock**: Upgrade jinja2 to 3.1.5
([`f833517`](https://github.com/populationgenomics/cpg-flow/commit/f8335170ce585158110283d2ecc2926f065c2ab9))

- **pyproject.toml,uv.lock**: Upgrade jinja2 as pip-audit logs
([`101bff5`](https://github.com/populationgenomics/cpg-flow/commit/101bff5becb27435819059f888dd9536efa5bfd3))

Continuous Integration

- **test.yaml,update-badges.yaml**: Add save badge data back to test
([`d2aab13`](https://github.com/populationgenomics/cpg-flow/commit/d2aab13f16853a69741d2f05174609c4b2a8558a))

- **update-badges.yaml**: Run after Test
([`22819cf`](https://github.com/populationgenomics/cpg-flow/commit/22819cf11266c5d8f407d9e77513109253e756cc))

- **.github/workflows/**: Change run order
([`84cfa2c`](https://github.com/populationgenomics/cpg-flow/commit/84cfa2cbee3da9659e9e99075f343a77b8efbb16))

- **package.yaml**: Run after update badges
([`de2fa6c`](https://github.com/populationgenomics/cpg-flow/commit/de2fa6c6147676072a8ba583885059d012b996c9))

- **web-docs.yaml**: Run after badge update
([`d986ecd`](https://github.com/populationgenomics/cpg-flow/commit/d986ecdd0330c59d2ef1cd8a7c74c169fb462e70))

- **package.yaml**: Run on completion of Test
([`d9af0a4`](https://github.com/populationgenomics/cpg-flow/commit/d9af0a42864ffee7716f2907ac0408c57638cb20))

- **package.yaml,web-docs.yaml**: Package on alpha/main only
([`4734447`](https://github.com/populationgenomics/cpg-flow/commit/4734447246f6e055c8e2c3264a69ed4a77db2f80))

Refactoring

- **.dummy**: Add file
([`4648964`](https://github.com/populationgenomics/cpg-flow/commit/464896412a0113ae6dc69025eb60e7344ee31aee))

Bug Fixes

- **pyproject.toml**: Import coloredlogs
([`6a875cf`](https://github.com/populationgenomics/cpg-flow/commit/6a875cf3e82009ee376d1e790b79993f440c927c))

- **docs/update_readme.py,pyproject.toml-,+7**: Fix linter warnings
([`97acdb8`](https://github.com/populationgenomics/cpg-flow/commit/97acdb8db163e29b31832d0ccc4219cce1dbf8cd))

Build System

- **pyproject.toml,uv.lock**: Add pyyaml
([`9171532`](https://github.com/populationgenomics/cpg-flow/commit/9171532d4c239a1c24e674b046ae68c89719f0a7))

Chores

- Update badges.yaml with test results and coverage
([`9304439`](https://github.com/populationgenomics/cpg-flow/commit/9304439f6d4d9da58f411917022378e8557b3f0f))

- Update badges.yaml with test results and coverage
([`db932a4`](https://github.com/populationgenomics/cpg-flow/commit/db932a461e39596a99cbdc81104a8c36f53008a7))

- Update badges.yaml with test results and coverage
([`a750689`](https://github.com/populationgenomics/cpg-flow/commit/a750689bbd61c98bf5a11a6ff0ff137dd3dc3936))

- Merge alpha
([`b009c47`](https://github.com/populationgenomics/cpg-flow/commit/b009c471b2e1e425d0f07de394fc83b86da7649b))

- Update badges.yaml with test results and coverage
([`ea440eb`](https://github.com/populationgenomics/cpg-flow/commit/ea440eb37ff244f04be2c5924e15032f5926a53a))

- Update badges.yaml with test results and coverage
([`16f13be`](https://github.com/populationgenomics/cpg-flow/commit/16f13be0d764ebd3f48d9b8f842bc3e845434dc6))

- Update badges.yaml with test results and coverage
([`eb8be5b`](https://github.com/populationgenomics/cpg-flow/commit/eb8be5bbc01d4b75cfd9b6a193d96d2721464d2b))

- Update badges.yaml with test results and coverage
([`d3f6b6b`](https://github.com/populationgenomics/cpg-flow/commit/d3f6b6ba013f29a0ed6b0e371f4223c278bb0a54))

Continuous Integration

- **.github/workflows/**: Package and web docs after test
([`adaa682`](https://github.com/populationgenomics/cpg-flow/commit/adaa682c990e87869e07c97a81d9ea6c2ce235b3))

- **update-badges.yaml**: Use env correctly
([`e337b5a`](https://github.com/populationgenomics/cpg-flow/commit/e337b5a97b45febdc30a0690e8d441aef7ddd482))

- **update-badges.yaml**: Use env variables
([`47bd7fd`](https://github.com/populationgenomics/cpg-flow/commit/47bd7fd4ab4167e32904700af49da93e63155979))

- **update-badges.yaml**: Save env variables to GITHUB_ENV
([`3816a41`](https://github.com/populationgenomics/cpg-flow/commit/3816a413035c27d19e9610b6d66a98eaa4809647))

- **update-badges.yaml**: Fix unzip
([`653851b`](https://github.com/populationgenomics/cpg-flow/commit/653851b79666e3ae6708ca7bdef03c7a8adea9d6))

- **update-badges.yaml**: List downloaded artifacts
([`2240494`](https://github.com/populationgenomics/cpg-flow/commit/2240494135cf38546b9dbd3e7356175f692690b6))

- **update-badges.yaml**: Custom download artifact
([`415a376`](https://github.com/populationgenomics/cpg-flow/commit/415a3762d79cee8cbbe9b373ce7391df584e90bd))

- **update-badges.yaml,docs/badges.yaml**: Custom download artifact
([`fb177f2`](https://github.com/populationgenomics/cpg-flow/commit/fb177f2a16e1e10ccdf6c982bd03e9630e107449))

- **test.yaml,update-badges.yaml**: Change to using artifacts
([`6fea9f6`](https://github.com/populationgenomics/cpg-flow/commit/6fea9f6c7a84582c9ae9888de1f7cd83634fe30d))

- **package.yaml**: Add step to update alpha on package of main
([`4d9eb8a`](https://github.com/populationgenomics/cpg-flow/commit/4d9eb8a06fac89570144504334dec1c85a31f161))

- **update-badges.yaml**: Checkout the branch so push works
([`2393d2a`](https://github.com/populationgenomics/cpg-flow/commit/2393d2a1c805654a2f2a03aed7066261c44606e6))

- **update-badges.yaml**: Checkout the triggering workflow ref
([`f1c09c9`](https://github.com/populationgenomics/cpg-flow/commit/f1c09c94cc3b681d0f3a94b5ceb77d9b8d29d5b0))

- **test.yaml,update-badges.yaml**: Merge main
([`01d6bd7`](https://github.com/populationgenomics/cpg-flow/commit/01d6bd7e3a0c1ce2b4ea732e36c18c31956517b9))

- **test.yaml,update-badges.yaml**: Add to default branch
([`20ca3a4`](https://github.com/populationgenomics/cpg-flow/commit/20ca3a47ed28a8fde5228c7a16e54275743fb086))

- **test.yaml,update-badges.yaml**: Back to workflow_run trigger
([`a1bed2d`](https://github.com/populationgenomics/cpg-flow/commit/a1bed2d93c02a0a92de3324d873efacef919e780))

- **test.yaml,update-badges.yaml**: Download manually
([`1375dd6`](https://github.com/populationgenomics/cpg-flow/commit/1375dd62c06c73dacdccb90477bd2e2f0e00c286))

- **update-badges.yaml**: Back to workflow_run
([`551bd32`](https://github.com/populationgenomics/cpg-flow/commit/551bd32d4f5aed67951e806f85188afb28ae9f0f))

- **test.yaml,update-badges.yaml**: Retry download-artifact
([`471c125`](https://github.com/populationgenomics/cpg-flow/commit/471c12597d4187480962601c1b91f981c6b09e73))

- **.github/workflows/,docs/**: Test workflow upload artifact
([`390d162`](https://github.com/populationgenomics/cpg-flow/commit/390d1622ae1e64e4d59c75c2e397616fbddfa07d))

- **update-badges.yaml**: Add token
([`0bd20ee`](https://github.com/populationgenomics/cpg-flow/commit/0bd20eec5232397e58b892acf192d7a88b6c72e5))

- **update-badges.yaml**: Try wait-for-test job
([`46cf28a`](https://github.com/populationgenomics/cpg-flow/commit/46cf28a718476d23e2ee65a58c30f7a01849b896))

- **update-badges.yaml**: Remove push trigger
([`d73a32b`](https://github.com/populationgenomics/cpg-flow/commit/d73a32b1c431af6cd234c81ffbfcd26cde47e40e))

- **update-badges.yaml**: Trigger on push to readme
([`4152cdf`](https://github.com/populationgenomics/cpg-flow/commit/4152cdf390922affa1b1756d959327b3eaac67e0))

- **update-badges.yaml**: Add manual run
([`ca01baf`](https://github.com/populationgenomics/cpg-flow/commit/ca01bafe8f98f3325299ec276b29dd43e347af5a))

- **web-docs.yaml**: Rename to kebab case
([`67b1e94`](https://github.com/populationgenomics/cpg-flow/commit/67b1e9422f3c1b3ea306182598bc5aea88c1d465))

- **.github/workflows/,docs/**: Mv update-badges from test workflow
([`3b90377`](https://github.com/populationgenomics/cpg-flow/commit/3b90377104969a03e2f2dda1127564a294b716a9))

Documentation

- **docs/alpha/**: Create the docs page
([`75e772e`](https://github.com/populationgenomics/cpg-flow/commit/75e772edee1095440008adff8b5d4d9e779ac891))

Refactoring

- **.dummy**: Dummy commit
([`258223b`](https://github.com/populationgenomics/cpg-flow/commit/258223b297fd327ac804c50d316edf518a896b07))

- **.dummy**: Dummy commit
([`62038c0`](https://github.com/populationgenomics/cpg-flow/commit/62038c03d17d779852c1fa2644d78f15b28a69af))

Bug Fixes

- **pyproject.toml,src/cpg_flow/inputs.py-,+10**: Use better logger
([`057ab0e`](https://github.com/populationgenomics/cpg-flow/commit/057ab0e17bebc0f07797bf695c64a74cdec15c14))

Chores

- Update badges.yaml with test results and coverage
([`792f640`](https://github.com/populationgenomics/cpg-flow/commit/792f64026d064cfb3e9bfac1f91ee32cb7c8239f))

- Update badges.yaml with test results and coverage
([`02011fe`](https://github.com/populationgenomics/cpg-flow/commit/02011fe31f8bc3e5662d62057f41615433104c19))

Continuous Integration

- **web_docs.yaml,Makefile**: Rm excessive permissions, fix script name
([`febaf9c`](https://github.com/populationgenomics/cpg-flow/commit/febaf9c92e5fc68b6157c791c68476a1880b2c70))

- **test.yaml**: Add git pull
([`f9477f6`](https://github.com/populationgenomics/cpg-flow/commit/f9477f62c580f91489acbe33bd3bf0bf4ab0b92e))

- **test.yaml**: Fix save badge env step
([`2a37f74`](https://github.com/populationgenomics/cpg-flow/commit/2a37f7420d23b4a8ee1a74f0e2a5990b702570d1))

- **test.yaml**: Fix for coverage_color calculation
([`a57972f`](https://github.com/populationgenomics/cpg-flow/commit/a57972f4dd151a98eab8ebb2c3bffa4846e78b10))

- **./,.github/workflows/,docs/**: Update badge values in test workflow
([`0f02c23`](https://github.com/populationgenomics/cpg-flow/commit/0f02c230f521b4901026a64d16383a7ce4fecc6c))

- **web_docs.yaml**: Only build docs on alpha and main
([`63adf12`](https://github.com/populationgenomics/cpg-flow/commit/63adf12c955419edac30c0cfcc971eb1b2105a51))

- **web_docs.yaml**: Add web doc deploy
([`b81dca5`](https://github.com/populationgenomics/cpg-flow/commit/b81dca5bcd1037876700be9b8015ade223c0e1b0))

- **test.yaml**: Fix coverage color logic
([`cd4a722`](https://github.com/populationgenomics/cpg-flow/commit/cd4a722a0950bd107f6d47f0f72488f5a1728d84))

- **test.yaml,README.md**: Create badges
([`630911b`](https://github.com/populationgenomics/cpg-flow/commit/630911b933833e26c88919843c636934ae88b64c))

Documentation

- **README.md**: Clean up
([`e22d96d`](https://github.com/populationgenomics/cpg-flow/commit/e22d96d17718b9836b44bf10afc6c4678a956a5b))

- **README.md**: Remove pip as suggestion
([`0a34d54`](https://github.com/populationgenomics/cpg-flow/commit/0a34d54d647fdd055f849426e8c0ddd0ac3f81e4))

- **CONTRIBUTING.md**: Add notes on commitlint and commitizen
([`8609727`](https://github.com/populationgenomics/cpg-flow/commit/8609727be4bfb5bcdd66c404473eeeae7b0c75d2))

- **README.md**: Add notes about commitlint and commitizen
([`396adc7`](https://github.com/populationgenomics/cpg-flow/commit/396adc742294c37a2ccbca8f318230ed65bf4dc3))

- **README.md**: Test badge
([`50ba1af`](https://github.com/populationgenomics/cpg-flow/commit/50ba1af626264e4aa29a9cd9d167c9d5bab7ba47))

- **./,.github/workflows/,docs/**: Replace badges, fix urls
([`97a7977`](https://github.com/populationgenomics/cpg-flow/commit/97a797732e6c86e9a84298b2c3356de323c7e57b))

- **DEVELOPERS.md,README.md**: Finish readme, rm old dev docs
([`a1e4676`](https://github.com/populationgenomics/cpg-flow/commit/a1e46767dc266e3fc811d54620923335ca6cae95))

- **./,.github/workflows/,docs/**: Document workflow update
([`3eff1de`](https://github.com/populationgenomics/cpg-flow/commit/3eff1deee0534005f2928fa6611de2c7e7fd3aad))

- **./,.github/workflows/**: Script to document all of our workflows
([`4ffadab`](https://github.com/populationgenomics/cpg-flow/commit/4ffadab227c2a27ffc3d960cb422d1dd064474c9))

- **web_docs.yaml,Makefile-,+22**: Generate docs on all branches
([`991cf57`](https://github.com/populationgenomics/cpg-flow/commit/991cf5783d7d35dee56a7ab0452d54e69c695c4e))

- **.pre-commit-config.yaml,Makefile,docs/**: Use pydoc to document api
([`341f0ff`](https://github.com/populationgenomics/cpg-flow/commit/341f0ff17e4a11b9805dc73a4a0e2bbe9e265d74))

Bug Fixes

- **target.py**: Add fix for alignment has to target
([`8e7b6a9`](https://github.com/populationgenomics/cpg-flow/commit/8e7b6a9268b3f09bd37d808f7720591305c24225))

- **src/cpg_flow/targets/**: Improve hashing efficiency
([`b3715e8`](https://github.com/populationgenomics/cpg-flow/commit/b3715e8b68d2fb58a3922730f845cd34e2325b68))

Bug Fixes

- **src/cpg_flow/,src/cpg_flow/targets/**: Add missing methods
([`22edaf2`](https://github.com/populationgenomics/cpg-flow/commit/22edaf2d1f07a3a456e16faa4dfd11b22f530d4c))

- **src/cpg_flow/status.py**: Cohort has no method .target_id
([`f5f2264`](https://github.com/populationgenomics/cpg-flow/commit/f5f22648d1996043521860075573d25f4804e261))

- **src/cpg_flow/metamist.py**: Create_analysis make id lists optional
([`b3ef85c`](https://github.com/populationgenomics/cpg-flow/commit/b3ef85cc9c14a8acf7e84227d931e76399b7110b))

- **src/cpg_flow/**: Add passing cohort ids to create analysis
([`d2fa675`](https://github.com/populationgenomics/cpg-flow/commit/d2fa67559f74e6e7ae1108611e3df5cd838179be))