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securebio

2 indexed repositories · View on GitHub

nao-mgs-workflow

Python · 30 stars
basecall-workflow
Nextflow workflow to run basecalling on Nanopore data

Nextflow · 0 stars

Beginner friendly Everything

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Alignment duplicate marking ignores strand and pair orientation Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 52/100

securebio/nao-mgs-workflow#993 · 1 comment · Opened Sep 3, 2026
Add an nf-test pinning CP/DP/UP behaviour across Bowtie2 and duplicate marking Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 48/100

securebio/nao-mgs-workflow#992 · 1 comment · Opened Sep 3, 2026
Publish an alignment end coordinate so half-mapped reads can be duplicate-grouped on evidence Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 55/100

securebio/nao-mgs-workflow#975 · 1 comment · Opened Sep 1, 2026
mark_duplicates ignores fragment length when the fragment is shorter than the read Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 58/100

securebio/nao-mgs-workflow#948 · 2 comments · Opened Aug 25, 2026
Three full-table sorts in SPLIT_VIRAL_TSV_BY_SELECTED_TAXID exist only as preconditions for streaming tools Open

enhancement repo:mgs-workflow time&cost

Difficulty 5/5 Over a week Newbie friendliness 45/100

securebio/nao-mgs-workflow#922 · 1 comment · Opened Aug 7, 2026
Evaluate faster alternatives to BLAST for viral hit validation Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

securebio/nao-mgs-workflow#920 · 1 comment · Opened Aug 6, 2026
Triage accumulated container CVEs (16 distinct HIGH/CRITICAL, mostly one shared base layer) Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 42/100

securebio/nao-mgs-workflow#914 · 1 comment · Opened Aug 5, 2026
Allow non-dev INDEX builds from the dev branch Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#878 · 2 comments · Opened Jul 7, 2026
NUCLEAZE: fail fast on binary/index version mismatch instead of hanging (follow-up to #867) Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#873 · 3 comments · Opened Jul 1, 2026
Follow up on ignored Trivy CVEs: patch as upstream fixes become reachable Open

repo:mgs-workflow

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

securebio/nao-mgs-workflow#870 · 1 comment · Opened Jul 1, 2026
Publish taxonomy-merged.dmp from the index workflow (enable taxid canonicalization) Open

repo:mgs-workflow

Difficulty 3/5 1-2 days Newbie friendliness 72/100

securebio/nao-mgs-workflow#863 · 1 comment · Opened Jun 29, 2026
Flaky test-subworkflows failure: nf-test JsonException (NUL byte) reading its own metadata under parallel execution Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 48/100

securebio/nao-mgs-workflow#862 · 1 comment · Opened Jun 28, 2026
Finalize Kraken domain-summary migration: drop legacy bracken naming and vestigial columns Open

repo:mgs-workflow

Difficulty 5/5 Over a week Newbie friendliness 35/100

securebio/nao-mgs-workflow#851 · 1 comment · Opened Jun 24, 2026
Bracken output is empty due to Kraken2 standard database taxonomy change breaking domain-level classification Open

repo:mgs-workflow

securebio/nao-mgs-workflow#841 · 1 comment · 1 assignee · Opened Jun 16, 2026
Add CI lint to catch process labels that match no `withLabel:` selector Open

repo:mgs-workflow

Difficulty 3/5 1-2 days Newbie friendliness 65/100

securebio/nao-mgs-workflow#826 · 1 comment · Opened Jun 8, 2026
csv.DictReader in add_conditional_tsv_column.py breaks on quality strings starting with " (reader-side analogue of #534) Open

bug priority_1 repo:mgs-workflow

securebio/nao-mgs-workflow#823 · 1 comment · 1 assignee · Opened Jun 5, 2026
Add golden-file integration test for benchmark_index.py write_summary_md Open

repo:mgs-workflow

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

securebio/nao-mgs-workflow#820 · 1 comment · Opened May 22, 2026
Consider writing DOWNSTREAM sentinel files when each group is complete Open

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

securebio/nao-mgs-workflow#817 · 2 comments · Opened May 20, 2026
Add nf-test coverage for the basecalling Nextflow workflow Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

securebio/basecall-workflow#26 · Opened May 14, 2026
Add pytest coverage for automation/run_automation.py Open

Difficulty 3/5 1-2 days Newbie friendliness 75/100

securebio/basecall-workflow#25 · Opened May 14, 2026
Migrate process `shell:` blocks to `script:` (Nextflow 25.04 deprecation) Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

securebio/basecall-workflow#24 · Opened May 13, 2026
Tune per-component thread counts in NUCLEAZE process Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#804 · 1 comment · Opened May 13, 2026
Map RUN workflow critical path and identify next-round perf candidates Open

repo:mgs-workflow

Difficulty 5/5 Over a week Newbie friendliness 35/100

securebio/nao-mgs-workflow#785 · 2 comments · Opened May 11, 2026
Swap pigz→rapidgzip on decompression hot paths Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 52/100

securebio/nao-mgs-workflow#776 · 1 comment · Opened May 11, 2026
Promote duplicate_reads_similarity.tsv.gz to expected DOWNSTREAM output and re-include in sentinel barrier Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 55/100

securebio/nao-mgs-workflow#731 · 1 comment · Opened Apr 22, 2026
Extract hardcoded BBDuk masking params into shared config Open

chimera detection repo:mgs-workflow

Difficulty 5/5 Over a week Newbie friendliness 35/100

securebio/nao-mgs-workflow#716 · 1 comment · Opened Apr 6, 2026
Move dev-only dependencies to optional-dependencies group Open

repo:mgs-workflow

Difficulty 3/5 1-2 days Newbie friendliness 52/100

securebio/nao-mgs-workflow#700 · 1 comment · Opened Mar 18, 2026
Hoist TSVFactory to module level for better type annotations Open

repo:mgs-workflow

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

securebio/nao-mgs-workflow#692 · 1 comment · Opened Mar 11, 2026
Asymmetric aligner column selection across natural/combined/artificial subsets Open

repo:mgs-workflow

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#669 · 1 comment · Opened Feb 19, 2026
Investigate whether Bracken added_reads can be negative Open

repo:mgs-workflow

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

securebio/nao-mgs-workflow#666 · 1 comment · Opened Feb 18, 2026
Compare nf-test results directly to golden data Open

repo:mgs-workflow

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

securebio/nao-mgs-workflow#663 · 1 comment · Opened Feb 16, 2026
Port long-running BBDuk processes to Nucleaze Open

enhancement repo:mgs-workflow time&cost

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

securebio/nao-mgs-workflow#655 · 1 comment · Opened Feb 12, 2026
Add sample name validation for safe filename characters Open

repo:mgs-workflow

Difficulty 3/5 1-2 days Newbie friendliness 52/100

securebio/nao-mgs-workflow#648 · 1 comment · Opened Feb 6, 2026
Fix inconsistent process.queue placement in ONT config files Open

bug repo:mgs-workflow

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

securebio/nao-mgs-workflow#625 · 1 comment · Opened Jan 29, 2026
Automate version bump on merge to main Open

read classification

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#616 · 1 comment · Opened Jan 28, 2026
Document CI checks Open

read classification

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

securebio/nao-mgs-workflow#614 · 1 comment · Opened Jan 28, 2026
Fix issues with version tracking Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

securebio/nao-mgs-workflow#601 · 1 comment · Opened Jan 24, 2026
Check outputs of integration tests match expected output lists Open

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

securebio/nao-mgs-workflow#599 · 1 comment · Opened Jan 23, 2026
Consider removing cross-delivery grouping Open

read classification

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

securebio/nao-mgs-workflow#596 · 2 comments · Opened Jan 22, 2026
Remove backwards compatibility for version tracking when no longer needed Open

read classification

Difficulty 4/5 3-5 days Newbie friendliness 28/100

securebio/nao-mgs-workflow#595 · 1 comment · Opened Jan 21, 2026
Clarify Github Actions triggers Open

read classification

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

securebio/nao-mgs-workflow#592 · 1 comment · Opened Jan 20, 2026
Switch tmp directory for sort commands Open

read classification

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

securebio/nao-mgs-workflow#587 · 4 comments · Opened Jan 19, 2026
Switch nao-dedup dependency to forthcoming rust-only version Open

read classification

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

securebio/nao-mgs-workflow#583 · 1 comment · Opened Jan 15, 2026
Similarity-based duplicate marking requires multiple steps to identify final exemplars Open

read classification

Difficulty 4/5 3-5 days Newbie friendliness 42/100

securebio/nao-mgs-workflow#582 · 1 comment · Opened Jan 15, 2026
Pipeline fails for samples with lots of vertebrate viral reads Open

read classification

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

securebio/nao-mgs-workflow#576 · 4 comments · Opened Jan 14, 2026
Switch ECR images to non-root user after build Open

read classification

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

securebio/nao-mgs-workflow#575 · 1 comment · Opened Jan 14, 2026
Publishing Fastp json reports to results Open

enhancement read classification

Difficulty 4/5 3-5 days Newbie friendliness 45/100

securebio/nao-mgs-workflow#574 · 7 comments · Opened Jan 14, 2026
Document or automate test data generation for complex processes Open

read classification

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

securebio/nao-mgs-workflow#573 · 1 comment · Opened Jan 14, 2026
Update Dorado version? Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

securebio/basecall-workflow#17 · 4 comments · Opened Jan 7, 2026
Add CLAUDE.md file Open

read classification

Difficulty 1/5 Under an hour Newbie friendliness 45/100

securebio/nao-mgs-workflow#565 · 1 comment · Opened Jan 5, 2026

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