hydra-genetics/hydra-genetics issues and pull requests

#273 - fix: handle location determination of repositories better for local m…

Pull Request - State: closed - Opened by Smeds over 1 year ago

#272 - feat: make it possible to entries without url when fetching data

Pull Request - State: closed - Opened by Smeds over 1 year ago

#271 - fix: set valid common container version in config.yaml

Pull Request - State: closed - Opened by padraicc over 1 year ago

#270 - fix: remove conda from template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#269 - chore: release 1.5.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#268 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#267 - fix: minor bug fixes

Pull Request - State: closed - Opened by Smeds over 1 year ago

#266 - A command in your Readme.md does not work

Issue - State: open - Opened by stela2502 over 1 year ago
Labels: bug

#265 - chore: release 1.5.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#264 - fix: revert incorrect path to `mkdocs.yaml`

Pull Request - State: closed - Opened by maehler over 1 year ago

#263 - fix: update readthedocs with correct mkdocs,yaml file name

Pull Request - State: closed - Opened by Smeds over 1 year ago

#262 - fix: incorrect path to `mkdocs.yaml`

Pull Request - State: closed - Opened by maehler over 1 year ago

#261 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#260 - fix: improve validation

Pull Request - State: closed - Opened by Smeds over 1 year ago

#259 - fix: handle case when array or number is passed to is_file

Pull Request - State: closed - Opened by Smeds over 1 year ago

#258 - feat: cli to fetch/validate reference data

Pull Request - State: closed - Opened by Smeds over 1 year ago - 1 comment

#257 - style: remove leading spaces in pipeline-template config

Pull Request - State: closed - Opened by elleira over 1 year ago

#256 - fix: add sys.exit if no --configfile

Pull Request - State: closed - Opened by elleira over 1 year ago

#255 - test: update pipeline template integration config

Pull Request - State: closed - Opened by elleira over 1 year ago

#254 - fix: make style check happy with regex in template for common.smk

Pull Request - State: closed - Opened by Smeds over 1 year ago

#253 - fix: update test links in template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#252 - fix: update snakefmt workflow to match latest template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#251 - fix: update dry-run workflow to match latest template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#250 - fix: update lint workflow to match current template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#249 - chore: release 1.4.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#248 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#247 - feat: update pipeline template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#246 - Leading spaces in pipeline config template

Issue - State: closed - Opened by maehler over 1 year ago

#245 - feat: remove dropna for units

Pull Request - State: closed - Opened by Smeds over 1 year ago

#244 - Wrong path to Snakefile in integration test instructions

Issue - State: open - Opened by maehler over 1 year ago
Labels: documentation

#243 - Module name hard-coded in README

Issue - State: open - Opened by maehler over 1 year ago
Labels: documentation

#242 - Default branch is not set correctly in github actions

Issue - State: open - Opened by maehler over 1 year ago - 1 comment
Labels: bug

#241 - feat: make read regex less stringent

Pull Request - State: closed - Opened by Smeds over 1 year ago

#240 - feat: update snakemake versionm allow range up to version 8

Pull Request - State: closed - Opened by Smeds over 1 year ago

#239 - Script flag for `create-rule`

Issue - State: open - Opened by maehler over 1 year ago
Labels: enhancement

#238 - docs: Update simple_pipeline.md

Pull Request - State: closed - Opened by nnneeennn over 1 year ago

#237 - Minimum snakemake version is not applied to `requirements.txt`

Issue - State: open - Opened by maehler over 1 year ago
Labels: bug

#236 - fix: add preserve timestamp to output rule function

Pull Request - State: closed - Opened by Smeds over 1 year ago

#235 - fix: cli spelling error

Pull Request - State: closed - Opened by Smeds over 1 year ago

#234 - feat: for pipeline template, change branch name master to main

Pull Request - State: closed - Opened by Smeds over 1 year ago

#233 - docs: Update skeleton_rule.smk message

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#232 - refactor: remove reference option from cli until we have something im…

Pull Request - State: closed - Opened by Smeds over 1 year ago

#231 - fix: sort entries in template resources.schema.yaml in alphabetically…

Pull Request - State: closed - Opened by Smeds over 1 year ago

#230 - chore: release 1.3.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#229 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#228 - docs: download test data later

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#227 - fix: make output work with yaml

Pull Request - State: closed - Opened by elleira over 1 year ago

#226 - docs: add missing \ to tutorial command

Pull Request - State: closed - Opened by Smeds over 1 year ago

#225 - fix: add missing library name and update variable name

Pull Request - State: closed - Opened by Smeds over 1 year ago

#224 - fix: update output list function

Pull Request - State: closed - Opened by Smeds over 1 year ago

#223 - docs: add command to download reference and fastq data from gdrive

Pull Request - State: closed - Opened by Smeds over 1 year ago

#222 - docs: update tutorial

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#221 - feat: update hydra-genetics version for template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#220 - docs: update tutorial

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#219 - chore: release 1.2.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#218 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#217 - refactor: Update units.schema.yaml

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#216 - fix: add abs path template for png copying

Pull Request - State: closed - Opened by Smeds over 1 year ago

#215 - refactor: update units.schema.yaml for pipeline template

Pull Request - State: closed - Opened by elleira over 1 year ago

#214 - fix: add barcode to units schema

Pull Request - State: closed - Opened by Smeds over 1 year ago

#213 - feat: output list/rule copy function added.

Pull Request - State: closed - Opened by Smeds over 1 year ago

#212 - fix: change to correct parameter name

Pull Request - State: closed - Opened by Smeds over 1 year ago

#211 - feat: remove dummy rule

Pull Request - State: closed - Opened by Smeds over 1 year ago

#210 - chore: release 1.1.0

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#209 - chore: dev to master

Pull Request - State: closed - Opened by Smeds over 1 year ago

#208 - feat: update click dep to match snakefmt versions

Pull Request - State: closed - Opened by Smeds over 1 year ago

#207 - feat: update project/module template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#206 - fix: config template

Pull Request - State: closed - Opened by jonca79 over 1 year ago

#205 - docs: remove martin as code owner

Pull Request - State: closed - Opened by Smeds over 1 year ago

#204 - fix: update requirements for pipeline template

Pull Request - State: closed - Opened by Smeds over 1 year ago

#203 - feat: cli to fetch containers and update config

Pull Request - State: closed - Opened by Smeds over 1 year ago

#202 - fix: replace iteritems() with items()

Pull Request - State: closed - Opened by maehler over 1 year ago

#201 - `pandas.Series.iteritems` is deprecated

Issue - State: closed - Opened by maehler over 1 year ago

#200 - `get_units` drops valid rows

Issue - State: open - Opened by maehler over 1 year ago

#199 - feat: drop conda support and testing

Pull Request - State: closed - Opened by Smeds over 1 year ago

#198 - refactor: remove unused code

Pull Request - State: closed - Opened by Smeds over 1 year ago

#197 - chore: release 1.0.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#196 - chore: dev to master

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#195 - feat!: force user to set index from which format field data will be extracted

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#194 - feat!: force user to set samplex index position

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#193 - feat: update project template

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#192 - docs: readthedocs for hydra

Pull Request - State: closed - Opened by jonca79 almost 2 years ago

#191 - github acion snakefmt fails since we have no master branch

Issue - State: open - Opened by elleira almost 2 years ago
Labels: bug

#190 - update config.yaml, samples.tsv and units.tsv

Issue - State: open - Opened by elleira almost 2 years ago - 1 comment
Labels: bug

#189 - feat: rename template integration file

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#188 - feat: update project template

Pull Request - State: closed - Opened by Smeds almost 2 years ago

#187 - chore: release 0.15.0

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 1 comment
Labels: autorelease: tagged

#186 - chore: dev to master

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

#185 - feat(comman): update workflow name regex

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

#184 - feat: function used to switch between github and local repos

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

#183 - fix: update warning raised when tools tries to calculate barcode sequ…

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

#182 - chore: release 0.14.1

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago - 1 comment
Labels: autorelease: tagged

#181 - chore: dev to master

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

#180 - fix(utils): update handling for retrieval of data using function

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

#179 - chore: release 0.14.0

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago - 1 comment
Labels: autorelease: tagged

#178 - chore: dev to master

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

#177 - feat: make it possible to select one ore more of specified data sources

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

#176 - fix: skeleton rule to pass snakefmt

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

#175 - chore: release 0.13.2

Pull Request - State: closed - Opened by github-actions[bot] over 2 years ago - 1 comment
Labels: autorelease: tagged

#174 - chore: dev to master

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

GitHub / hydra-genetics/hydra-genetics issues and pull requests