Skip to content

Issues: broadinstitute/long-read-pipelines

Periodically remove stale branches
#132 opened May 26, 2020 by SHuang-Broad
Open 4
Workflow Documentation
#424 opened Sep 20, 2023 by bshifaw
Open 3
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

95 Open 66 Closed
95 Open 66 Closed
Author
Filter by author
Label
Filter by label
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Milestones
Filter by milestone
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Make preemption dependent on expected length
#442 opened Jan 26, 2024 by SHuang-Broad
API to pull WDL documentation from Dockstore to Terra documentation
#441 opened Jan 23, 2024 by SHuang-Broad
Prep for SMRTLink v13
#439 opened Dec 1, 2023 by SHuang-Broad
@SHuang-Broad
Install samtools with libdeflate enabled optimization
#436 opened Nov 23, 2023 by SHuang-Broad
1
Use sysmetic monitor to check GCP's preemption rates
#434 opened Nov 20, 2023 by SHuang-Broad
1
Update Dockerfiles for Faster Conda Dependency Resolution
#433 opened Oct 31, 2023 by bshifaw
Make the finalization tasks take a manifest
#432 opened Oct 24, 2023 by SHuang-Broad
bump DV version to 1.6
#431 opened Oct 24, 2023 by SHuang-Broad
@SHuang-Broad
lr-metrics docker refers to a non-official build of GATK help wanted Extra attention is needed optimization
#427 opened Sep 27, 2023 by SHuang-Broad
@kvg
Assembly pipeline output should give bgz files not gz files high priority High priority
#426 opened Sep 27, 2023 by SHuang-Broad
@SHuang-Broad
Documentation for Epi and CNV pipelines documentation
#425 opened Sep 21, 2023 by SHuang-Broad
2 tasks
@SHuang-Broad
Workflow Documentation
#424 opened Sep 20, 2023 by bshifaw
@kvg @tedsharpe
@bshifaw @SHuang-Broad @fabio-cunial
3
Migrate all viable docker images to google artifact registry
#419 opened Aug 21, 2023 by bshifaw
Long read pipeline Canu issue with Mouse Genome reference
#416 opened Aug 12, 2023 by nikhil777shingte
2
Make Finalize.wdl tasks volatile
#414 opened Aug 7, 2023 by jamesemery
update all pacbio software to those packaged in the SMRTLink release
#407 opened May 5, 2023 by SHuang-Broad
ONTProcessBasecall Input Issue
#401 opened Apr 24, 2023 by hangsuUNC
Investigate if finalization steps could be improved with gcloud storage cp good first issue Good for newcomers optimization
#400 opened Apr 18, 2023 by SHuang-Broad
CNV pipeline needs to finalize results bug Something isn't working
#399 opened Apr 13, 2023 by SHuang-Broad
@SHuang-Broad
Replace LRConvertBCF workflow with a more efficient and up-to-date solution
#395 opened Apr 7, 2023 by bshifaw
@kvg
Go through the outputs of miniwdl check to clean up review-party things to be handled in the next review party
#394 opened Apr 6, 2023 by SHuang-Broad
Consider saving WGS FASTQ outputs in CoLoRd format good first issue Good for newcomers optimization
#387 opened Mar 10, 2023 by SHuang-Broad
Next iteration of WDL validator should enforce documentation documentation
#385 opened Mar 9, 2023 by SHuang-Broad
1
Review lr-utils conda / python envs.
#354 opened Jul 28, 2022 by jonn-smith
1
Complete implementation of lr-ref
#353 opened Jul 28, 2022 by jonn-smith
ProTip! Exclude everything labeled bug with -label:bug.