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mskcc/beagle

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Voyager Backend

Is mskcc/beagle beginner-friendly?

The maintainers of mskcc/beagle usually reply to a pull request within 3 days. 1 beginner-friendly issue is open now.

Stars
2
Forks
7
Open beginner issues
1
Indexed issues
99
Avg merge
6d 16m
Merged PRs (30d)
8
Dominant language
Python
License
Apache-2.0
Last GitHub push
Sep 25, 2026
Latest indexed
Sep 19, 2026
No contributing guide
No code of conduct
Beginner labels
help wanted

How to contribute to mskcc/beagle

  1. There is no contributing guide, so start from the README and a few recently merged pull requests to see how changes are proposed.
  2. It ships a Dockerfile or Docker Compose file, so you can run it without installing its whole toolchain.
  3. Your contributions will be published under the project's Apache-2.0 license.
  4. Pick the open beginner-friendly issue below and comment that you want to work on it before you start.
Beginner friendly Everything
Open All

Issues somebody may already be working on are listed last. List everything by date

  • Remove all harded references to juno
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 68/100

    mskcc/beagle#1500 ·

    Maintainers usually reply within 3 days

  • How will strict syntax affect repo
    May be free again Open
    • Is something wrong?

    mskcc/beagle#1493 · 1 assignee ·

    Maintainers usually reply within 3 days

  • Update mock metadata
    May be free again Open
    • Is something wrong?

    mskcc/beagle#1125 · 1 assignee ·

    Maintainers usually reply within 3 days

  • Cannot logout of admin on swagger page
    Open
    • Is something wrong?
    bug

    Difficulty 2/5 1-3 hours Newbie friendliness 35/100

    mskcc/beagle#1122 ·

    Maintainers usually reply within 3 days

  • tempo-mpgen column names inconsistent with schema
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    mskcc/beagle#1068 · 1 comment ·

    Maintainers usually reply within 3 days

  • Operator errors are hidden in the logs
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    mskcc/beagle#1058 ·

    Maintainers usually reply within 3 days

  • Approved users does not populate the user model
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    mskcc/beagle#1053 ·

    Maintainers usually reply within 3 days

  • Cannot log out as admin
    Open
    • Is something wrong?
    bug

    Difficulty 2/5 1-3 hours Newbie friendliness 25/100

    mskcc/beagle#1052 ·

    Maintainers usually reply within 3 days

  • Replace User Specific Paths on Jinja Template
    May be free again Open
    • Is something wrong?

    mskcc/beagle#1034 · 1 assignee ·

    Maintainers usually reply within 3 days

  • Github Repo page for Tempo
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 25/100

    mskcc/beagle#1030 ·

    Maintainers usually reply within 3 days

  • Need to updated paths
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 45/100

    mskcc/beagle#1028 · 1 comment ·

    Maintainers usually reply within 3 days

  • checking if historical pairing file was de-synced
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    mskcc/beagle#996 ·

    Maintainers usually reply within 3 days

  • Check isCmoRequest flag on import
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 25/100

    mskcc/beagle#987 ·

    Maintainers usually reply within 3 days

  • Jobs restarted through the retry endpoint start with resume_attempts 0
    Open
    • Is something wrong?
    bug

    Difficulty 2/5 1-3 hours Newbie friendliness 35/100

    mskcc/beagle#984 ·

    Maintainers usually reply within 3 days

  • Job restart failed to submit if job_store is cleaned up
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 20/100

    mskcc/beagle#963 ·

    Maintainers usually reply within 3 days

  • Notifier search does not search on status
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 45/100

    mskcc/beagle#939 ·

    Maintainers usually reply within 3 days

  • Modified_date should have db_index=true
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 35/100

    mskcc/beagle#929 ·

    Maintainers usually reply within 3 days

  • Queries on created_date do not work
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 15/100

    mskcc/beagle#928 ·

    Maintainers usually reply within 3 days

  • Add migration to backfill jira ids to jobgroups
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 25/100

    mskcc/beagle#927 ·

    Maintainers usually reply within 3 days

  • Need to backfill deliveryDate metadata on empty fields
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 20/100

    mskcc/beagle#926 ·

    Maintainers usually reply within 3 days

  • Many of the jobgroup jira_id fields are empy
    Open
    • Is something wrong?
    bug

    Difficulty 3/5 1-2 days Newbie friendliness 45/100

    mskcc/beagle#925 ·

    Maintainers usually reply within 3 days

  • Handle JIRA status when 0 samples are imported
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 25/100

    mskcc/beagle#924 ·

    Maintainers usually reply within 3 days

  • Number of runs that complete differs from the number of runs that succeeded in OperatorRun
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    mskcc/beagle#920 ·

    Maintainers usually reply within 3 days

  • Some pooled normal fastq files show up twice in the mapping file
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 30/100

    mskcc/beagle#917 ·

    Maintainers usually reply within 3 days

  • Elastic apm configuration parameters should be set through env
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 38/100

    mskcc/beagle#915 ·

    Maintainers usually reply within 3 days

  • Assign study id(s) to sample metadata, IMPACT/HemePACT data sets mostly
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    mskcc/beagle#891 ·

    Maintainers usually reply within 3 days

  • Refactor runner/tasks to work with abstract RunObjects in order to support Nextflow
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 30/100

    mskcc/beagle#888 ·

    Maintainers usually reply within 3 days

  • [MetaDB] Separate NATS job into different queue
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 45/100

    mskcc/beagle#887 ·

    Maintainers usually reply within 3 days

  • [MetaDB] - Change deploy script to start NATS listening job
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    mskcc/beagle#886 ·

    Maintainers usually reply within 3 days

  • Update helix filters operator output directory
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    mskcc/beagle#885 ·

    Maintainers usually reply within 3 days

  • Argos operator - need to fix pairing with pooled normals through /v0/run/operator/pairs
    Open
    • Is something wrong?
    bug

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    mskcc/beagle#884 ·

    Maintainers usually reply within 3 days

  • Missing conflict reasons
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 45/100

    mskcc/beagle#880 ·

    Maintainers usually reply within 3 days

  • filter_redact=True behavior inconsistent; what is expected behavior
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 20/100

    mskcc/beagle#877 ·

    Maintainers usually reply within 3 days

  • Restarting jobs with updates to inputs
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 20/100

    mskcc/beagle#875 ·

    Maintainers usually reply within 3 days

  • Standardize logging for Celery tasks
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    mskcc/beagle#863 ·

    Maintainers usually reply within 3 days

  • Hiseq Rapid Run and Hiseq High Output conflict
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    mskcc/beagle#854 · 4 comments ·

    Maintainers usually reply within 3 days

  • For ETL, assign dirs, subdirs, and files being moved to CMO storage space to group cmoigo
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    mskcc/beagle#846 ·

    Maintainers usually reply within 3 days

  • Add PipelineType
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 35/100

    mskcc/beagle#843 ·

    Maintainers usually reply within 3 days

  • Pipeline Completed before all runs are completed
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    mskcc/beagle#833 ·

    Maintainers usually reply within 3 days

  • Fix started time for runs
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 10/100

    mskcc/beagle#826 · 1 comment ·

    Maintainers usually reply within 3 days

  • Job notification when an operator receives bad inputs errors out
    Open
    • Is something wrong?

    Difficulty 2/5 1-3 hours Newbie friendliness 55/100

    mskcc/beagle#821 ·

    Maintainers usually reply within 3 days

  • Deployment strategy for Voyager
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 15/100

    mskcc/beagle#820 · 1 comment ·

    Maintainers usually reply within 3 days

  • Updated metadata JSON from beagle_etl sometimes don't output all json files into directory
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 25/100

    mskcc/beagle#806 ·

    Maintainers usually reply within 3 days

  • Use Batch call to get Status of Job from Ridgeback
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 30/100

    mskcc/beagle#803 ·

    Maintainers usually reply within 3 days

  • Put work dir, lsf.log, input.json paths in Jira comments
    Open
    • Is something wrong?

    Difficulty 3/5 1-2 days Newbie friendliness 35/100

    mskcc/beagle#801 · 1 comment ·

    Maintainers usually reply within 3 days

  • Regex query does not seem to be working
    May be free again Open
    • Is something wrong?

    mskcc/beagle#786 · 1 assignee ·

    Maintainers usually reply within 3 days

  • parallelize access operators
    Open
    • Is something wrong?

    Difficulty 5/5 Over a week Newbie friendliness 25/100

    mskcc/beagle#785 ·

    Maintainers usually reply within 3 days

  • Index table and endpoint for autocomplete
    Open
    • Is something wrong?

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    mskcc/beagle#777 ·

    Maintainers usually reply within 3 days

  • Value queries on the same field should be treated as OR queries
    May be free again Open
    • Is something wrong?

    mskcc/beagle#775 · 3 comments · 1 assignee ·

    Maintainers usually reply within 3 days

  • Configure LSF walltime per Run
    Open
    • Is something wrong?
    enhancement

    Difficulty 4/5 3-5 days Newbie friendliness 35/100

    mskcc/beagle#742 ·

    Maintainers usually reply within 3 days

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