Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / remiolsen/anglerfish issues and pull requests
#85 - Misc. improvements, unit tests and mypy proofing
Pull Request -
State: open - Opened by kedhammar 20 days ago
- 2 comments
Labels: enhancement
#84 - Readability improvements
Pull Request -
State: closed - Opened by kedhammar about 1 month ago
#83 - Finalising 0.7 release
Pull Request -
State: closed - Opened by remiolsen about 2 months ago
#82 - add the anglerfish ascii to the command line output :P
Issue -
State: closed - Opened by FranBonath 3 months ago
- 2 comments
Labels: enhancement
#81 - Switch CLI over to typer, change command to "anglerfish run"
Pull Request -
State: closed - Opened by remiolsen 3 months ago
#80 - A more lenient lenient mode
Issue -
State: open - Opened by remiolsen 3 months ago
Labels: enhancement
#79 - More opinionated checks and warnings pushed to the anglerfish report
Issue -
State: open - Opened by remiolsen 4 months ago
Labels: enhancement
#78 - Update PyPi build-and-publish github action
Issue -
State: open - Opened by remiolsen 5 months ago
Labels: invalid
#77 - Bug fix for lenient mode and prepare release of 0.6.1
Pull Request -
State: closed - Opened by remiolsen 5 months ago
#76 - Bugfix explore again (this time to master)
Pull Request -
State: closed - Opened by alneberg 5 months ago
#75 - Anglerfish unkown indices list should contain the name of the closest sample(s) in the samplesheet and their edit distance
Issue -
State: closed - Opened by remiolsen 5 months ago
Labels: enhancement
#74 - Explore command should compare adaptor sequences and collapse results for identical ones
Issue -
State: open - Opened by alneberg 5 months ago
#73 - Umi format explore fix
Pull Request -
State: closed - Opened by alneberg 5 months ago
#72 - Add UMI support
Pull Request -
State: closed - Opened by remiolsen 5 months ago
- 2 comments
#71 - Bugfix: Explore command mixed the two adaptor ends together in the dataframe
Pull Request -
State: closed - Opened by alneberg 5 months ago
#70 - Merge dev
Pull Request -
State: closed - Opened by remiolsen 5 months ago
#69 - Move this repository to NationalGenomicsInfrastructure org
Issue -
State: open - Opened by remiolsen 5 months ago
- 2 comments
Labels: question
#68 - Allow user to determine the Anglerfish run dir name exactly
Issue -
State: closed - Opened by kedhammar 5 months ago
Labels: enhancement
#67 - Add my poster from the "Visualize Your Science" course, for fun
Pull Request -
State: closed - Opened by kedhammar 5 months ago
#66 - Tidy up paf stats and umatch and match counts
Issue -
State: open - Opened by remiolsen 5 months ago
Labels: bug
#65 - Support for multiprocessed fastq output
Pull Request -
State: closed - Opened by remiolsen 5 months ago
- 3 comments
#64 - Report the total number of unmatched reads
Issue -
State: open - Opened by remiolsen 5 months ago
Labels: enhancement
#63 - Lenient mode tweaks
Issue -
State: closed - Opened by remiolsen 5 months ago
- 1 comment
Labels: bug
#62 - Fix debug output
Pull Request -
State: closed - Opened by remiolsen 5 months ago
- 1 comment
#61 - Convert to click CLI
Issue -
State: closed - Opened by remiolsen 5 months ago
Labels: enhancement, good first issue
#60 - Add support for .bam input
Issue -
State: open - Opened by remiolsen 6 months ago
Labels: enhancement, low priority
#59 - First version of the explore command
Pull Request -
State: closed - Opened by alneberg 6 months ago
- 2 comments
#58 - Adapt Dockerfile for arm64 and some requirements changes
Pull Request -
State: closed - Opened by alneberg 6 months ago
#57 - Samplesheet-free mode
Issue -
State: open - Opened by remiolsen 6 months ago
- 1 comment
Labels: enhancement
#56 - Changed conda env to development only
Pull Request -
State: closed - Opened by remiolsen 6 months ago
#55 - Change requirements to python>=3.10
Pull Request -
State: closed - Opened by remiolsen 6 months ago
#54 - Implement continous integration practices + formatting and fixes across entire repo
Pull Request -
State: closed - Opened by kedhammar 6 months ago
- 1 comment
#53 - Added: Force rev. complement and lenient mode scaling
Pull Request -
State: closed - Opened by remiolsen 7 months ago
Labels: enhancement
#52 - Dev 0.6
Pull Request -
State: closed - Opened by remiolsen 7 months ago
#51 - Write extensive documentation
Issue -
State: open - Opened by remiolsen 7 months ago
Labels: enhancement
#50 - Parallelise lenient mode
Issue -
State: closed - Opened by remiolsen 7 months ago
Labels: enhancement, low priority
#49 - Add github action things
Issue -
State: closed - Opened by remiolsen 7 months ago
- 1 comment
Labels: low priority
#48 - Move to python 3.10
Issue -
State: closed - Opened by remiolsen 7 months ago
Labels: good first issue, low priority
#47 - Set number of unknown indices to be equal to length of samplesheet
Issue -
State: closed - Opened by remiolsen 8 months ago
Labels: enhancement
#46 - Parse ONT metadata from fastq files
Issue -
State: open - Opened by remiolsen 8 months ago
Labels: enhancement, low priority
#45 - Duplicate sample names are allowed some times
Issue -
State: closed - Opened by remiolsen 8 months ago
Labels: bug
#44 - Add ONT barcode aware mode
Issue -
State: closed - Opened by remiolsen 8 months ago
Labels: bug, enhancement
#43 - Fix debug output
Issue -
State: closed - Opened by remiolsen 10 months ago
Labels: bug
#42 - Use custom adaptor templates from command-line
Issue -
State: open - Opened by remiolsen 10 months ago
Labels: enhancement
#41 - Report 0 matching samples
Issue -
State: closed - Opened by remiolsen 10 months ago
Labels: bug
#40 - Decouple reporting from "main" loop
Issue -
State: closed - Opened by remiolsen 10 months ago
Labels: enhancement
#39 - Master dataframe output
Issue -
State: closed - Opened by remiolsen 10 months ago
- 1 comment
Labels: enhancement, help wanted
#38 - Support indices with UMIs
Issue -
State: closed - Opened by remiolsen 10 months ago
- 1 comment
Labels: enhancement
#37 - Consider all orientations of I5 and I7 indices
Issue -
State: closed - Opened by remiolsen 11 months ago
- 4 comments
Labels: enhancement
#36 - Add pyyaml as a dependency; used by the samplesheet module
Pull Request -
State: closed - Opened by cbrueffer about 1 year ago
- 1 comment
#34 - Add max unknown indices parameter
Pull Request -
State: closed - Opened by remiolsen over 1 year ago
#33 - Kedhammar/config
Pull Request -
State: closed - Opened by kedhammar over 1 year ago
- 1 comment
#32 - Add parameter for maximum number of unknown indexes to output
Issue -
State: closed - Opened by remiolsen almost 2 years ago
Labels: enhancement
#31 - Bump numpy to 1.22.0
Issue -
State: closed - Opened by remiolsen almost 2 years ago
Labels: dependencies
#30 - Handle glob patterns and multiple fastq file input in samplesheet
Issue -
State: closed - Opened by remiolsen almost 2 years ago
Labels: enhancement
#29 - Bump numpy from 1.21.0 to 1.22.0
Pull Request -
State: closed - Opened by dependabot[bot] about 2 years ago
- 1 comment
Labels: dependencies
#28 - Make adapter templates configurable
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: enhancement
#27 - Add config file
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: enhancement
#26 - Add description to pypi
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: enhancement
#25 - Misc. refactoring
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: enhancement
#24 - Finalise 0.4.2
Pull Request -
State: closed - Opened by remiolsen over 2 years ago
- 1 comment
#23 - Bump numpy from 1.19.2 to 1.21.0
Pull Request -
State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies
#22 - 0.4.2-rc.1
Pull Request -
State: closed - Opened by remiolsen over 2 years ago
#21 - version 0.4.2 rc.1
Pull Request -
State: closed - Opened by remiolsen over 2 years ago
#20 - 0.4.2 More bugfixes and automation
Issue -
State: closed - Opened by remiolsen over 2 years ago
- 1 comment
Labels: bug, enhancement
#19 - Fix apt change release
Pull Request -
State: closed - Opened by remiolsen over 2 years ago
#18 - Dev -> version 0.4.1
Pull Request -
State: closed - Opened by remiolsen over 2 years ago
#17 - Remove baked-in fastQC and MultiQC
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: invalid
#16 - Sort paf stats into a proper json array
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: enhancement
#15 - Fix undetermined indexes when only one sample in samplesheet
Issue -
State: closed - Opened by remiolsen over 2 years ago
Labels: bug
#14 - 0.4.0 Changes
Pull Request -
State: closed - Opened by remiolsen almost 3 years ago
#13 - Output csv file
Issue -
State: closed - Opened by remiolsen about 3 years ago
Labels: enhancement
#12 - Output the commandline arguments
Issue -
State: closed - Opened by remiolsen over 3 years ago
#11 - Automatically adjust minimum mismatches allowed
Issue -
State: closed - Opened by remiolsen over 3 years ago
#10 - Independently calculate read lengths
Issue -
State: closed - Opened by remiolsen almost 4 years ago
Labels: enhancement
#9 - 0.3.0 release
Pull Request -
State: closed - Opened by remiolsen about 4 years ago
#8 - Output: Simulate illumina reads
Issue -
State: open - Opened by ewels about 4 years ago
#7 - Screen for all known illumina adapters
Issue -
State: closed - Opened by ewels about 4 years ago
- 1 comment
#6 - Summarize all anglerfish sample read counts in one table
Issue -
State: closed - Opened by remiolsen over 4 years ago
- 1 comment
Labels: enhancement
#5 - Redesign input samplesheet
Issue -
State: closed - Opened by remiolsen over 4 years ago
Labels: enhancement
#4 - Possibility have multiple Ilmn index types in one samplesheet
Issue -
State: closed - Opened by remiolsen over 4 years ago
Labels: bug, enhancement
#3 - Multi-thread fastq read/write operations
Issue -
State: closed - Opened by remiolsen over 4 years ago
Labels: enhancement
#2 - Release version 0.2.0
Pull Request -
State: closed - Opened by remiolsen over 4 years ago
#1 - Make README with ASCII artwork
Issue -
State: closed - Opened by ewels over 4 years ago
- 2 comments
Labels: wontfix