Ecosyste.ms: Issues

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

GitHub / looselab/readfish issues and pull requests

#391 - Use `.get` instead of `[]` for strand classifcations

Pull Request - State: open - Opened by Adoni5 12 days ago
Labels: enhancement

#390 - Sort out logger in `read_until_client/base.py`

Issue - State: open - Opened by Adoni5 12 days ago
Labels: enhancement

#389 - Not supporting MinKNOW 6.2.8

Issue - State: open - Opened by HaxyMoly 15 days ago - 6 comments
Labels: bug

#388 - Approach to estimate enrichment with playback

Issue - State: open - Opened by DanteV19 3 months ago - 1 comment

#386 - PromethION R10 (5kHz) Bulk fast5

Issue - State: closed - Opened by imsuneth 4 months ago - 2 comments

#384 - Catch some "placeholder" channel positions being 0 on flongle

Pull Request - State: closed - Opened by Adoni5 6 months ago - 1 comment

#383 - Fix issue340 - live TOML handling

Pull Request - State: closed - Opened by Adoni5 6 months ago

#382 - Minor change to readme to better reflect update to 6.0 and deprecatio…

Pull Request - State: closed - Opened by mattloose 6 months ago - 2 comments

#381 - Delete dc918797-33da-4414-9999-eb9132d22971_readfish.tsv

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

#380 - Delete dc918797-33da-4414-9999-eb9132d22971_readfish.tsv

Pull Request - State: closed - Opened by Adoni5 6 months ago

#379 - Issue365/flongle draw split

Pull Request - State: closed - Opened by Adoni5 6 months ago

#378 - Revert "Fix #365"

Pull Request - State: closed - Opened by Adoni5 6 months ago

#377 - bump all node 16 actions to node 20

Pull Request - State: closed - Opened by Adoni5 6 months ago - 1 comment

#376 - feature py3.12 support

Issue - State: open - Opened by Adoni5 6 months ago - 4 comments
Labels: enhancement, good first issue, idea

#375 - chore: drop python 3.8

Issue - State: closed - Opened by Adoni5 6 months ago - 3 comments
Labels: Stale, chore

#374 - Feature/deprecate guppy

Pull Request - State: closed - Opened by Adoni5 6 months ago

#372 - reads not unblocking as expected

Issue - State: closed - Opened by shair89 6 months ago - 8 comments

#371 - toml_live not updated upon changes

Issue - State: closed - Opened by lborcard 6 months ago - 6 comments

#370 - Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:

Issue - State: closed - Opened by adbeggs 6 months ago - 18 comments
Labels: Stale

#369 - DRAFT Feature/minknow6 compatibility

Pull Request - State: closed - Opened by Adoni5 6 months ago - 2 comments

#368 - Detect native adaptive sampling and warrn.

Issue - State: open - Opened by mattloose 6 months ago - 1 comment
Labels: enhancement

#367 - Question: Correct configuration for switching off barcodes

Issue - State: closed - Opened by philipschoettler 6 months ago - 9 comments

#366 - Fix #365

Pull Request - State: closed - Opened by Adoni5 7 months ago - 1 comment
Labels: Stale

#365 - Readfish is not running for Flongle Playback Data

Issue - State: closed - Opened by Nirmal2310 7 months ago - 9 comments

#363 - High count of no-barcode that map to my targets

Issue - State: closed - Opened by lborcard 8 months ago - 15 comments
Labels: question

#362 - next release candidate checklist

Issue - State: open - Opened by Adoni5 8 months ago
Labels: enhancement, epic

#361 - Feature/pass reads

Pull Request - State: closed - Opened by Adoni5 8 months ago - 2 comments

#360 - chore: update FAQ

Issue - State: open - Opened by Adoni5 8 months ago
Labels: enhancement, good first issue, chore

#359 - Dorado Alignments

Pull Request - State: closed - Opened by Adoni5 8 months ago - 1 comment
Labels: Stale

#358 - Error with flongle flow cell splitting

Issue - State: closed - Opened by Dcwrenn 8 months ago - 6 comments
Labels: bug

#357 - comparison between MinKNOW and Readfish

Issue - State: closed - Opened by ylang0825 8 months ago - 4 comments
Labels: question

#355 - chore: update github workflow actions

Issue - State: closed - Opened by alexomics 9 months ago - 1 comment
Labels: enhancement, good first issue, chore

#354 - Change Duplex version to 2024.1.0

Pull Request - State: closed - Opened by Adoni5 9 months ago

#353 - Having only one region in toml caused issue

Issue - State: closed - Opened by jennieli421 9 months ago - 13 comments
Labels: Stale

#352 - add live poly a and skip poly a feature

Pull Request - State: closed - Opened by satriobio 9 months ago - 2 comments
Labels: Stale

#351 - Feature/check minknow

Pull Request - State: closed - Opened by mattloose 10 months ago - 10 comments

#350 - Circular Binary Segmentation

Issue - State: closed - Opened by tom-murray98 10 months ago - 3 comments

#349 - Detect MinKNOW version and warn.

Issue - State: closed - Opened by mattloose 10 months ago - 1 comment
Labels: enhancement

#347 - Problem communicating with basecaller after MinKnow update

Issue - State: closed - Opened by gc-content 10 months ago - 10 comments
Labels: bug, good first issue

#347 - Problem communicating with basecaller after MinKnow update

Issue - State: open - Opened by gc-content 10 months ago - 1 comment
Labels: bug, good first issue

#345 - Playback issue

Issue - State: closed - Opened by alexomics 10 months ago - 14 comments

#345 - Playback issue

Issue - State: closed - Opened by alexomics 10 months ago - 14 comments

#344 - Dorado plugin

Pull Request - State: closed - Opened by mattloose 10 months ago - 6 comments

#344 - Introducing a dorado specific plugin which handles the change from on…

Pull Request - State: open - Opened by mattloose 10 months ago - 1 comment

#343 - Question about Readfish basecalling performance for messy samples

Issue - State: open - Opened by jamesemery 11 months ago - 4 comments
Labels: documentation

#343 - Question about Readfish basecalling performance for messy samples

Issue - State: closed - Opened by jamesemery 11 months ago - 6 comments
Labels: documentation, Stale

#341 - Depletion setting and unexpected behavior

Issue - State: closed - Opened by jennieli421 11 months ago - 2 comments

#340 - toml_live handling issue

Issue - State: closed - Opened by mattloose 11 months ago
Labels: bug

#340 - toml_live handling issue

Issue - State: open - Opened by mattloose 11 months ago
Labels: bug

#339 - location of readfish output

Issue - State: closed - Opened by bjaysheel 12 months ago - 4 comments
Labels: question, Stale

#338 - Provide additional TOML files which provide examples of host depletion and other use cases for readfish.

Issue - State: open - Opened by mattloose 12 months ago
Labels: documentation, enhancement

#337 - Not being able to finish the tutorial/test

Issue - State: closed - Opened by franztastic 12 months ago - 6 comments

#336 - readfish with just depletion?

Issue - State: closed - Opened by josephhughes 12 months ago - 4 comments
Labels: question, Stale

#335 - Readfish and boss-runs in 2024

Issue - State: closed - Opened by jelber2 12 months ago - 3 comments
Labels: question

#334 - readfish stats on-target median read length and N50 always 0B

Issue - State: closed - Opened by maximilianmordig 12 months ago - 4 comments
Labels: question, Stale

#333 - Example barcode balancing

Issue - State: closed - Opened by ahfitzpa 12 months ago - 7 comments
Labels: documentation, Stale

#332 - Error when validating if the name of the reference genome contains dots

Issue - State: closed - Opened by bernatgel about 1 year ago - 3 comments

#330 - Adding additional .mmi extensions to all possible fasta file format l…

Pull Request - State: closed - Opened by mattloose about 1 year ago - 9 comments

#329 - Readfish intermittently crashes during barcoded experiment

Issue - State: open - Opened by jamesemery about 1 year ago - 5 comments
Labels: bug

#328 - Validation of decisions listed in `Barcodes`/`Regions` in Toml

Issue - State: open - Opened by Adoni5 about 1 year ago - 1 comment
Labels: bug, enhancement

#327 - Change type on --wait-for-ready to int

Pull Request - State: closed - Opened by Adoni5 about 1 year ago

#326 - readfish validate reference file name check

Issue - State: closed - Opened by speleonut about 1 year ago - 3 comments
Labels: enhancement

#325 - readfish stats

Issue - State: closed - Opened by alexomics about 1 year ago - 8 comments
Labels: Stale

#324 - Feature/duplex

Pull Request - State: closed - Opened by Adoni5 about 1 year ago - 5 comments

#323 - Fix changing directory after 60 seconds if no run folder

Pull Request - State: closed - Opened by Adoni5 about 1 year ago - 2 comments

#322 - Sequencing summary files for human genome experiment

Issue - State: closed - Opened by maximilianmordig about 1 year ago - 8 comments
Labels: question, Stale

#321 - Question: Determining Required Percentage Similarity and Handling Database Input

Issue - State: closed - Opened by ahfitzpa about 1 year ago - 5 comments
Labels: Stale

#319 - Close Mention of iter_align and iter_cent in common Gotcha's #302

Pull Request - State: closed - Opened by Adoni5 about 1 year ago - 2 comments
Labels: Stale

#318 - cannot find guppy_6 branch

Issue - State: closed - Opened by bjaysheel about 1 year ago - 3 comments

#317 - Duplex plugin

Issue - State: closed - Opened by Adoni5 about 1 year ago - 1 comment
Labels: enhancement, idea

#314 - Extend waiting up to 60 seconds time limit to 300 seconds for folder to appear

Issue - State: closed - Opened by Adoni5 about 1 year ago - 1 comment
Labels: bug

#313 - Closes issue #312

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

#312 - Unblock time incorrectly specified as int

Issue - State: closed - Opened by mattloose over 1 year ago - 1 comment
Labels: bug

#310 - Issue309

Pull Request - State: closed - Opened by mattloose over 1 year ago - 3 comments

#309 - Bulkfile links don't work in docs

Issue - State: closed - Opened by mattloose over 1 year ago - 1 comment

#308 - Argument should be in base args?

Issue - State: closed - Opened by mattloose over 1 year ago - 6 comments
Labels: Stale, needs discussion

#306 - Implement filtering of base calls and alignments

Pull Request - State: closed - Opened by Adoni5 over 1 year ago - 2 comments
Labels: Stale

#305 - Filtering implementation epic

Issue - State: open - Opened by Adoni5 over 1 year ago - 16 comments
Labels: enhancement, epic, needs discussion

#304 - Document `_filter.py`

Issue - State: closed - Opened by Adoni5 over 1 year ago - 1 comment
Labels: work-item, Stale

#303 - Markdown fixes

Issue - State: closed - Opened by Adoni5 over 1 year ago - 3 comments
Labels: documentation, epic, Stale

#302 - Mention of iter_align and iter_cent in common Gotcha's

Issue - State: closed - Opened by Adoni5 over 1 year ago - 4 comments
Labels: Stale

#301 - Move Changelog to docs/CHANGELOG.md

Issue - State: open - Opened by Adoni5 over 1 year ago - 1 comment
Labels: enhancement, idea

#300 - Updating README to address Apple Silicon grpcio issues.

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

#299 - Issue289/fix-region-requirement and add Changelog

Pull Request - State: closed - Opened by Adoni5 over 1 year ago
Labels: bug-fix

#298 - Names are confusing in the stats module

Issue - State: open - Opened by Adoni5 over 1 year ago
Labels: enhancement, idea

#297 - Resolve barcode region issue.

Issue - State: closed - Opened by mattloose over 1 year ago - 1 comment
Labels: bug

#296 - Fix logo src in README.md

Pull Request - State: closed - Opened by Adoni5 over 1 year ago

#295 - Update CI.yml

Pull Request - State: closed - Opened by Adoni5 over 1 year ago

#293 - Can't have external dependencies on PyPI

Issue - State: closed - Opened by Adoni5 over 1 year ago
Labels: bug

#292 - Hotfix/vendored-read-until

Pull Request - State: closed - Opened by Adoni5 over 1 year ago - 1 comment

#290 - Fix CI deployment failing to find /dist (maybe)

Pull Request - State: closed - Opened by Adoni5 over 1 year ago

#289 - Barcoded adaptive sampling not working as expected

Issue - State: closed - Opened by jamesemery over 1 year ago - 11 comments

#287 - Fix broken refactor links

Pull Request - State: closed - Opened by Adoni5 over 1 year ago

#286 - BUG: long reads segfault stats

Issue - State: open - Opened by Adoni5 over 1 year ago
Labels: bug, skill-issue

#285 - readfish stats crashes without indicating why if fed promethION data without the --prom flag

Issue - State: closed - Opened by mattloose over 1 year ago - 3 comments
Labels: bug, wontfix

#284 - Provide PromethION Bulkfiles

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

#283 - Issue273/README fixes and HTML stats

Pull Request - State: closed - Opened by mattloose over 1 year ago - 2 comments