ssi-dk/bifrost issues and pull requests

#85 - Documentation link at readme.md yields a 404

Issue - State: open - Opened by KasperThystrup almost 2 years ago

#84 - Change to support S.sonnei as E.coli on ariba_mlst and removing symlinks

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

#83 - Adding kma_pointmutations and reslab_stamper

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

#81 - chewBBACA component for Bifrost

Issue - State: closed - Opened by finngl almost 3 years ago - 4 comments
Labels: bifrost, Blocked

#80 - QC score

Issue - State: open - Opened by finngl over 3 years ago - 4 comments

#79 - Update submodule hashes

Pull Request - State: closed - Opened by githubz0r over 3 years ago

#78 - move bifrostlib and resfinder to latest commits

Pull Request - State: closed - Opened by githubz0r over 3 years ago

#77 - Requirements not passed failing the component

Issue - State: open - Opened by martinbaste almost 4 years ago
Labels: 🐛 bug

#76 - Fix for bifrost_run_launcher test will affect other tests as calling run_program isn't neccesary or desired now

Issue - State: closed - Opened by kimleeng almost 4 years ago

#75 - Adjust sample_component path to include final path not just sample path

Issue - State: open - Opened by kimleeng almost 4 years ago

#74 - Create version tag for all components and check dockerhub (update github actions)that it reflects properly

Issue - State: closed - Opened by kimleeng almost 4 years ago - 1 comment

#73 - turn bifrost into bifrostlib submodule and reporter submodule so that bifrost is just the collection and documentation organization

Issue - State: closed - Opened by kimleeng almost 4 years ago

#72 - Update datahandling.py

Pull Request - State: closed - Opened by kimleeng almost 4 years ago

#71 - push newest bifrostlib to all components

Issue - State: open - Opened by kimleeng almost 4 years ago

#70 - Fix issue where a component requirement isn't working. Currently it's checking off it's own id and not that of the target.

Issue - State: closed - Opened by kimleeng almost 4 years ago
Labels: 🐛 bug, 📲 api

#69 - custom run creation basic functionality

Pull Request - State: closed - Opened by martinbaste about 4 years ago

#68 - Split tests into fast and slow (or unit/integration) so that the watchdog runs quick ones first and then bigger ones after for faster feedback loops

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 🤖 automation

#67 - Update tests with new bifrostlib functionality

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 📲 api, 💾 data schemes, 🤖 automation

#66 - Update bifrostlib for samplecomponents to reflect schema2.0 and beyond, right now its more hardcoded for snakemake purposes

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 📲 api, 💾 data schemes

#65 - Add input species for components with a species requirement. This is so if the user changes the species the component still has info on which species it ran against

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🔨 pipelines

#64 - Download finders result for selected samples as csv

Issue - State: open - Opened by martinbaste about 4 years ago
Labels: 🏞 dashboard

#63 - Columns can be added/hidden by the user

Issue - State: open - Opened by martinbaste about 4 years ago
Labels: 🏞 dashboard

#62 - Clean up setup folder. shouldnt be needed but currently dockerfiles in others are pulling common resources from it. Should move those into the components (or base)

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 🐛 bug, 🔨 pipelines, 😊 verified

#61 - Change it so components can be re-installed onto themselves (for development adjustments to config.yaml) as deleting from DB to update is less than ideal.

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 🔨 pipelines, 🗄 database

#60 - Dockerize run_launcher

Pull Request - State: closed - Opened by kimleeng about 4 years ago

#59 - Fix setup to install indexes for DB and species install.

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 🗄 database

#58 - create a docker for bifrost launcher

Issue - State: closed - Opened by kimleeng about 4 years ago - 1 comment
Labels: 🔨 pipelines

#57 - Add old azure devops CI/CD into github actions

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 🤖 automation

#56 - Fix bug in container automation and add more for latest and dev

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 🐛 bug, 🤖 automation

#55 - Create github actions for creating docker images on release tags

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 🤖 automation

#54 - Mountable output folder for docker images

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement

#53 - 2.0.6 release

Pull Request - State: closed - Opened by kimleeng about 4 years ago

#52 - Run class not checking against run name properly

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 🐛 bug, 💾 data schemes, 😊 verified

#51 - Establish test data set which can be attached via mongo atlas

Issue - State: closed - Opened by kimleeng about 4 years ago - 1 comment
Labels: 🤗 data sharing, 🖥 server

#50 - Add species interface for managing species and alias's

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 📑 duplicate, 💪 enhancement, 🏞 dashboard

#49 - Update documentation to reflect schema2.0

Issue - State: closed - Opened by kimleeng about 4 years ago - 1 comment
Labels: 📝 documentation

#48 - Convert user feedback into a sample component

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 🔨 pipelines

#47 - Generate requirements for a validation set

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 👾 other

#46 - Look into anonymization mappings for fields

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 💪 enhancement, 🤗 data sharing, 💾 data schemes

#45 - Add a interface for managing species and there mappings

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard

#44 - Create github actions to automate testing

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🤖 automation

#43 - Adjust it so that components store installation path

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 💾 data schemes

#42 - Port over non public components for schema 2.0

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💥 invalid, 🔨 pipelines

#41 - Unify classes and api for different DB requests and api into one location

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 📲 api

#40 - Add loading bars/spinners to data tables if possible

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard

#39 - Look into showing contigs/coverage in a more intuitive way

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard

#38 - Change data plots for QC to show a pregenerated density plot

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 💪 enhancement, 🏞 dashboard

#37 - Adjust docker images to utilize a scratch folder

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 💪 enhancement, 🖥 server

#36 - Adjust components to have a unique name based on name, version, db_date

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 💾 data schemes

#35 - Add a wideview for the QC dashboard

Issue - State: closed - Opened by kimleeng about 4 years ago - 1 comment
Labels: 💪 enhancement, 🏞 dashboard

#34 - Ability to submit job requests to server from dashboard

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 🏞 dashboard, 📲 api, 🖥 server

#33 - Run components on samples to fill out DB when server isn't busy

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 📲 api, 🖥 server

#32 - Add the functionality of 'tags' into bifrost

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard, 💾 data schemes

#31 - Have the run checker default to be sorted by sample name and supplying lab

Issue - State: open - Opened by kimleeng about 4 years ago - 1 comment
Labels: 💪 enhancement, 🏞 dashboard

#30 - Create github shields for bifrost repo

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 📝 documentation

#29 - API for checking run status

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 📲 api

#28 - Ability to create a collection of runs through the UI

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard, 📲 api

#27 - Add a clear job list button

Issue - State: open - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard

#25 - Add a reason text box for supplying lab feedback

Issue - State: closed - Opened by kimleeng about 4 years ago
Labels: 💪 enhancement, 🏞 dashboard

#19 - cleaning up branches

Pull Request - State: closed - Opened by kimleeng about 4 years ago

#18 - Update install.sh, move samtools to env.yaml #16

Pull Request - State: closed - Opened by martinbaste almost 5 years ago

#17 - Update bifrost_for_install_full.yaml fix #14

Pull Request - State: closed - Opened by martinbaste almost 5 years ago

#16 - reorder conda environment channels

Issue - State: closed - Opened by corburn almost 5 years ago - 1 comment

#15 - install.sh was not updated when install directory was renamed setup

Issue - State: closed - Opened by corburn almost 5 years ago - 1 comment

#14 - pypi bifrostlib out-of-sync with repository bifrostlib

Issue - State: closed - Opened by corburn almost 5 years ago - 1 comment

#13 - remove_run.py unavailable

Issue - State: closed - Opened by corburn almost 5 years ago - 1 comment

#12 - Check what dev changes there are

Pull Request - State: closed - Opened by kimleeng almost 5 years ago

#11 - fix nan priority and nan group/species issues fix AB#529 fix AB#530

Pull Request - State: closed - Opened by martinbaste almost 5 years ago

#10 - sort runs by names fix AB#453

Pull Request - State: closed - Opened by martinbaste about 5 years ago

#9 - some performance improvements to fix AB#452

Pull Request - State: closed - Opened by martinbaste about 5 years ago

#8 - provided species flexibility AB#433

Pull Request - State: closed - Opened by martinbaste about 5 years ago

#7 - fix AB#430

Pull Request - State: closed - Opened by martinbaste over 5 years ago

#6 - Dev

Pull Request - State: closed - Opened by martinbaste over 5 years ago

#5 - Should fix the tests

Pull Request - State: closed - Opened by martinbaste over 5 years ago

#4 - Added code to allow email post run

Pull Request - State: closed - Opened by kimleeng over 5 years ago

#3 - Installation files

Pull Request - State: closed - Opened by kimleeng over 5 years ago

#2 - Add install file (rudementary)

Pull Request - State: closed - Opened by kimleeng over 5 years ago

#1 - Implementation of cge_mlst components

Pull Request - State: closed - Opened by kimleeng over 5 years ago

GitHub / ssi-dk/bifrost issues and pull requests