MDU-PHL/abritamr issues and pull requests

#44 - Understanding annotation seemingly discrepant to output

Issue - State: open - Opened by infinity-a11y 5 months ago

#43 - Create LICENSE

Pull Request - State: open - Opened by WhoisDonlee 5 months ago

#42 - Update db 2024 08 12

Pull Request - State: closed - Opened by kristyhoran 6 months ago

#41 - Issue with installing abritamr via Conda due to version and dependency conflicts

Issue - State: open - Opened by gdemoro 7 months ago

#40 - Update 2024 06 18

Pull Request - State: closed - Opened by kristyhoran 8 months ago

#39 - Updates 2024 02 23

Pull Request - State: closed - Opened by kristyhoran 12 months ago

#38 - Create python-publish.yml

Pull Request - State: open - Opened by kristyhoran about 1 year ago

#37 - moved archived database versions to top level - too large for pypi

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

#36 - Can you explain the the code a bit?

Issue - State: open - Opened by butterbee about 1 year ago - 1 comment

#35 - Update db 2023 10 12

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

#34 - Update Collate.py

Pull Request - State: open - Opened by abcdtree over 1 year ago

#33 - new issue for testing

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

#32 - test 2 for planner

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

#31 - Test Issue for planner

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

#30 - abritamr should fail with non-zero exit code if the amrfinder command is not successful

Issue - State: closed - Opened by bernt-matthias over 1 year ago - 5 comments
Labels: investigating

#29 - parallel: not found

Issue - State: closed - Opened by MHassanSaeed over 1 year ago - 2 comments

#28 - How to run program

Issue - State: open - Opened by peflanag over 1 year ago - 2 comments
Labels: documentation

#27 - duplicated sample ID in the input file resulted in a large

Issue - State: open - Opened by Wang-Jing-NZ almost 2 years ago
Labels: enhancement

#26 - Difficulty in running the abritamr report

Issue - State: closed - Opened by vmevada102 almost 2 years ago - 5 comments

#25 - Missing interpretation in the Salmonella report

Issue - State: open - Opened by Bio-finder almost 2 years ago
Labels: enhancement

#24 - Documentation improvement

Issue - State: open - Opened by Bio-finder almost 2 years ago
Labels: documentation

#23 - Unable to run abritamr in batch mode , giving error parallel: invalid option -- '-'

Issue - State: closed - Opened by ranjanmanishblue about 2 years ago - 3 comments
Labels: investigating

#22 - add license

Issue - State: closed - Opened by phiweger about 2 years ago - 1 comment

#21 - TypeError: sequence item 0: expected str instance, NoneType found

Issue - State: closed - Opened by milly-newton about 2 years ago

#20 - Meaningful test/validation

Issue - State: closed - Opened by kristyhoran over 2 years ago
Labels: documentation, verification

#19 - Fix docker build

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

#18 - POINTN causing None error

Issue - State: closed - Opened by kristyhoran over 2 years ago - 1 comment

#17 - Fix v1.0.7 tag

Issue - State: closed - Opened by pansapiens over 2 years ago

#16 - Need to check for empty dicts

Issue - State: closed - Opened by jdeligt about 3 years ago

#15 - Updating bioconda command

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

#14 - add identity option

Issue - State: closed - Opened by kristyhoran over 3 years ago
Labels: feature request

#13 - Add gene classes to salmonella mdu

Issue - State: closed - Opened by kristyhoran over 3 years ago
Labels: enhancement, verification

#12 - Update DB to 2021-09-30.1

Issue - State: closed - Opened by kristyhoran over 3 years ago
Labels: feature request, verification

#11 - Remove restriction on running with a different DB version

Issue - State: closed - Opened by kristyhoran over 3 years ago
Labels: feature request

#10 - Provide a combined output file

Issue - State: closed - Opened by kristyhoran over 3 years ago

#9 - missing blaEC gene

Issue - State: closed - Opened by kristyhoran over 3 years ago - 1 comment
Labels: bug

#8 - correct installation instructions

Issue - State: closed - Opened by Koen-vdl over 3 years ago - 1 comment

#7 - Issue with snakemake pipeline?

Issue - State: closed - Opened by jhawkey over 3 years ago - 6 comments

#6 - Teardown and rebuild

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

#5 - Bump jinja2 from 2.10.3 to 2.11.3

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#4 - Fix issues 2 and 3

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

#3 - Can't find `collate.py` when running within a Singularity container

Issue - State: closed - Opened by andersgs about 5 years ago

#2 - Path to Singularity image should be in config

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

#1 - Use click instead of argparse

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

GitHub / MDU-PHL/abritamr issues and pull requests