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

#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

#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

#35 - Dev

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

#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