NationalGenomicsInfrastructure anglerfish issues

NationalGenomicsInfrastructure / anglerfish

Anglerfish - Nanopore reads from Illumina libraries

MIT License

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issues

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Modularize explore

#91 alneberg opened 5 days ago
0
Strange truncation of fastq files when demultiplexing short Illumina inserts libraries

#90 j0n0curry opened 2 weeks ago
2
add sample indexes to report

#89 FranBonath opened 3 weeks ago
2
add more metadata in the anglerfish report

#88 FranBonath opened 3 weeks ago
3
Finalise 0.7 release

#87 remiolsen closed 3 weeks ago
2
Objectify and improve structuring

#86 kedhammar closed 1 month ago
0
Misc. improvements, unit tests and mypy proofing

#85 kedhammar closed 2 months ago
2
Readability improvements

#84 kedhammar closed 3 months ago
0
Finalising 0.7 release

#83 remiolsen closed 3 months ago
0
add the anglerfish ascii to the command line output :P

#82 FranBonath closed 4 months ago
2
Switch CLI over to typer, change command to "anglerfish run"

#81 remiolsen closed 4 months ago
0
A more lenient lenient mode

#80 remiolsen opened 5 months ago
0
More opinionated checks and warnings pushed to the anglerfish report

#79 remiolsen opened 6 months ago
0
Update PyPi build-and-publish github action

#78 remiolsen opened 7 months ago
0
Bug fix for lenient mode and prepare release of 0.6.1

#77 remiolsen closed 7 months ago
0
Bugfix explore again (this time to master)

#76 alneberg closed 7 months ago
0
Anglerfish unkown indices list should contain the name of the closest sample(s) in the samplesheet and their edit distance

#75 remiolsen closed 3 months ago
0
Explore command should compare adaptor sequences and collapse results for identical ones

#74 alneberg opened 7 months ago
0
Umi format explore fix

#73 alneberg closed 7 months ago
0
Add UMI support

#72 remiolsen closed 7 months ago
2
Bugfix: Explore command mixed the two adaptor ends together in the dataframe

#71 alneberg closed 7 months ago
0
Merge dev

#70 remiolsen closed 7 months ago
0
Move this repository to NationalGenomicsInfrastructure org

#69 remiolsen closed 3 weeks ago
2
Allow user to determine the Anglerfish run dir name exactly

#68 kedhammar closed 3 months ago
0
Add my poster from the "Visualize Your Science" course, for fun

#67 kedhammar closed 7 months ago
0
Tidy up paf stats and umatch and match counts

#66 remiolsen opened 7 months ago
0
Support for multiprocessed fastq output

#65 remiolsen closed 5 months ago
3
Report the total number of unmatched reads

#64 remiolsen opened 7 months ago
0
Lenient mode tweaks

#63 remiolsen closed 7 months ago
1
Fix debug output

#62 remiolsen closed 7 months ago
1
Convert to click CLI

#61 remiolsen closed 4 months ago
0
Add support for .bam input

#60 remiolsen opened 7 months ago
0
First version of the explore command

#59 alneberg closed 7 months ago
2
Adapt Dockerfile for arm64 and some requirements changes

#58 alneberg closed 7 months ago
0
Samplesheet-free mode

#57 remiolsen opened 8 months ago
1
Changed conda env to development only

#56 remiolsen closed 8 months ago
0
Change requirements to python>=3.10

#55 remiolsen closed 8 months ago
0
Implement continous integration practices + formatting and fixes across entire repo

#54 kedhammar closed 8 months ago
1
Added: Force rev. complement and lenient mode scaling

#53 remiolsen closed 9 months ago
0
Dev 0.6

#52 remiolsen closed 9 months ago
0
Write extensive documentation

#51 remiolsen opened 9 months ago
0
Parallelise lenient mode

#50 remiolsen closed 4 months ago
0
Add github action things

#49 remiolsen closed 8 months ago
1
Move to python 3.10

#48 remiolsen closed 8 months ago
0
Set number of unknown indices to be equal to length of samplesheet

#47 remiolsen closed 9 months ago
0
Parse ONT metadata from fastq files

#46 remiolsen opened 10 months ago
0
Duplicate sample names are allowed some times

#45 remiolsen closed 9 months ago
0
Add ONT barcode aware mode

#44 remiolsen closed 9 months ago
0
Fix debug output

#43 remiolsen closed 7 months ago
0
Use custom adaptor templates from command-line

#42 remiolsen opened 1 year ago
0