Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Clinical-Genomics/mutacc issues and pull requests

#107 - Fix picard version in Dockerfile

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 3 comments

#106 - Picard version not found makes Dockerfile fail build

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: bug

#105 - Fix workflow step version in Docker push action

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#104 - Broken push to Docker on release action

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: bug

#103 - Fix path to relevant coverage files in coveralls step of actions

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#102 - Updated python to v3.11 in Dockerfile and MongoDB to v7 in docker-compose

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#101 - Update python to 3.11 in Dockerfile

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: enhancement

#100 - Replace deprecated pkg_resources lib with importlib_resources

Pull Request - State: closed - Opened by northwestwitch about 1 year ago

#99 - Deprecated pkg_resources package warning

Issue - State: closed - Opened by northwestwitch about 1 year ago

#98 - Unfreeze pymongo and add integration test with MongoDB v7

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#97 - Move coverage to GitHub action and fix Docker push action

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 1 comment

#96 - Error in Docker Hub push action

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: bug

#95 - Fix broken installation by using Python>=3.8

Pull Request - State: closed - Opened by northwestwitch about 1 year ago - 2 comments

#94 - Broken badge on README page

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: bug

#93 - Python 3.6 no longer installed by conda when installing the software

Issue - State: closed - Opened by northwestwitch about 1 year ago
Labels: bug

#92 - cyvcf2/cyvcf2.pyx:1466:32: Cannot assign type 'double' to 'int'

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: bug

#91 - unfreeze PyMongo

Issue - State: closed - Opened by northwestwitch about 1 year ago - 1 comment
Labels: enhancement

#89 - Move tests and coverage to the GitHub actions

Pull Request - State: closed - Opened by northwestwitch almost 3 years ago - 2 comments

#87 - Freeze PyMongo to version < 4.0

Issue - State: closed - Opened by northwestwitch almost 3 years ago

#86 - Fix pypi push token info once again (and create a new release)

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

#85 - Fixed name of the token used by PyPI push action

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

#84 - Prepare new minor version 1.6

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#83 - Speed up Docker image building by basing it on a cyvcf2 image

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#81 - Multi-stage optimized -SMALLER- Dockerimage

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#80 - Coverage is 0%

Issue - State: open - Opened by northwestwitch about 3 years ago - 1 comment
Labels: bug

#79 - Fix deprecated yaml loader

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#78 - Speed-up Dockerimage building by starting from a cyvcf2-based image

Issue - State: closed - Opened by northwestwitch about 3 years ago
Labels: enhancement

#77 - Update the dependecy to use a fixed version of mongo-adapter

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#76 - Prepare version 1.5

Pull Request - State: closed - Opened by northwestwitch about 3 years ago - 6 comments

#75 - Add a CLI option to connect to DB URIs

Pull Request - State: closed - Opened by dnil about 3 years ago - 5 comments

#74 - Run Docker commands as non-root user and created docker-compose file

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

#73 - YAMLLoadWarning: deprecated call to function

Issue - State: closed - Opened by northwestwitch about 3 years ago - 2 comments
Labels: bug

#72 - Create a Docker-compose file that uses MongoDB version 4.4

Issue - State: closed - Opened by northwestwitch about 3 years ago - 1 comment

#71 - feat(vcf_filter): adds filter to vcf header

Pull Request - State: closed - Opened by jemten almost 4 years ago - 3 comments

#70 - Make mutacc-cg integration simpler

Issue - State: open - Opened by adrosenbaum over 4 years ago

#69 - Handling of SVs

Issue - State: open - Opened by adrosenbaum over 4 years ago

#68 - Get reads from sv

Pull Request - State: closed - Opened by adrosenbaum over 4 years ago - 2 comments

#67 - Add dockerfle

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 1 comment

#66 - Refactoring of code

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 1 comment

#65 - parent name should always be string

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 1 comment

#64 - Remove hardcode specific to Clinical Genomics

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 6 comments

#63 - Docker

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 1 comment

#62 - Get affected sibling

Pull Request - State: closed - Opened by adrosenbaum almost 5 years ago - 1 comment

#61 - Dynamic vcf parse

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 6 comments

#60 - Update documentation

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 1 comment

#59 - Get variant type (SV|SNV) from vcf

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 1 comment

#58 - Develop

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 1 comment

#57 - Allow user to make options based queries on some parameters such as v…

Pull Request - State: closed - Opened by adrosenbaum about 5 years ago - 1 comment

#56 - Version

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#55 - Code owners

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#54 - Stupid thing, really

Issue - State: closed - Opened by northwestwitch over 5 years ago

#53 - Demo

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

#52 - Including a demo?

Issue - State: closed - Opened by northwestwitch over 5 years ago

#51 - Allow for updating existing cases, and version fastq-files generated …

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#50 - Change from using 'pickle' modlule to serialize data for later use,

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#49 - Initiate gitflow

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#48 - fix yaml requirements

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#47 - Give json formated stdout for export, to be used by other tools using…

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#46 - Add rank model version for each variant

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#44 - Pep8

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#43 - Give binaries in config. Calculate 'padding' dynamically

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#42 - PEP8

Issue - State: closed - Opened by adrosenbaum over 5 years ago

#41 - First version

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#40 - Support for single end reads

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#39 - Added docstrings, remove unnecessary code, update README

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#38 - change location of directories and files generated by mutacc

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#37 - Extract more meta-data on variants from vcf

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#36 - Query

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#35 - Change in utils/bam_handler.py to better handle reads with missing mates.

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#34 - Improving VCF parsing

Pull Request - State: closed - Opened by adrosenbaum over 5 years ago - 1 comment

#33 - New cli

Pull Request - State: closed - Opened by adrosenbaum almost 6 years ago - 1 comment

#32 - adding more tests and removing unused code

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#31 - Final changes before test on rasta

Issue - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment
Labels: to discuss

#30 - remove command added.

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#29 - changes in vcf parsing

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#28 - Readme update

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#27 - Additional tests and travis configuration for repo.

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#26 - make system calls to command line tools more robust

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#25 - Exporting functionality added

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#24 - Extract reads from bam directly, change in collection schemas

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#23 - Exclude reads from fastq 'background' files

Issue - State: closed - Opened by adrosenbaum about 6 years ago - 2 comments
Labels: to discuss

#22 - Some changes in mutacc/utils/fastq_handler.py

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#21 - Readme

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#20 - Tests, logging, and cli functionality

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#19 - Thoughts on what to be stored in the mongodb

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#18 - Discuss how to deal with structural variants

Issue - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment
Labels: to discuss

#17 - Function to handle variants, and to parse cases

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#16 - GET READ NAME FROM BAM AND FIND READ IN FASTQ

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#15 - REDEFINING INPUT FOR MUTACC IMPORT

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#14 - SPECIFYING INPUT FOR MUTACC IMPORT

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#13 - ADDED SIMPLE FUNCTIONS FOR RETRIEVING INFO FROM SCOUT AND HOUSEKEEPER

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago - 1 comment

#12 - write get_causative_variants_from_scout

Issue - State: closed - Opened by henrikstranneheim about 6 years ago - 2 comments

#11 - write map_sample_ID

Issue - State: closed - Opened by henrikstranneheim about 6 years ago - 1 comment

#10 - Write get_file_from_housekeeper function

Issue - State: closed - Opened by henrikstranneheim about 6 years ago

#9 - ADDING TO CLI FUNCTIONALITY

Pull Request - State: closed - Opened by adrosenbaum about 6 years ago

#8 - Get Files from HouseKeeper

Issue - State: closed - Opened by adrosenbaum about 6 years ago