Issues

• map_reads process fails due to SAM/BAM mismatch when using :dev Docker container

  formbio/laava#128 · Filter by author jeremy-at-asimov opened on Dec 15, 2025

• possible bug in full-gap detection

  formbio/laava#113 · Filter by author rpdarst4 opened on Sep 17, 2025

• Question about full-gap classification.

  formbio/laava#105 · Filter by author Ilike0reos opened on Jun 12, 2025

• Critical Input Error: Fails to validate any input format for BAM files

  formbio/laava#104 · Filter by author SooryaChandra opened on Jun 8, 2025

• Request: Improved Documentation for Pipeline Input Files

  formbio/laava#96 · Filter by author CharlesARoy opened on Apr 9, 2025
  2

• With cpus=1, handle TSV post-processing safely

  bug
  formbio/laava#90 · Filter by author etal opened on Feb 27, 2025 · Next

• Use Quarto instead of Rmarkdown

  formbio/laava#88 · Filter by author etal opened on Feb 26, 2025

• Configure laava_dev as a proper development container (devcontainer)

  formbio/laava#85 · Filter by author etal opened on Feb 12, 2025 · Planned

• Consolidate the output metadata TSV for multi-sample runs

  formbio/laava#84 · Filter by author etal opened on Feb 12, 2025

• Nanopore reads, input convert it to FASTQ format

  question
  formbio/laava#82 · Filter by author dgoswamia opened on Feb 10, 2025
  2

• Include instrument name in output metadata TSV

  formbio/laava#80 · Filter by author etal opened on Feb 10, 2025 · Next

• Reduce laava Docker image size

  good first issue
  formbio/laava#76 · Filter by author etal opened on Jan 30, 2025
  5

• Add vector_type to output metadata TSV

  formbio/laava#59 · Filter by author etal opened on Sep 20, 2024 · Next
  2

• Subset output BAMs following v3 semantics

  formbio/laava#57 · Filter by author etal opened on Sep 5, 2024 · Planned

• Lambda normalization

  formbio/laava#55 · Filter by author etal opened on Aug 23, 2024

• Option for circular genome alignment and counting

  formbio/laava#54 · Filter by author etal opened on Aug 15, 2024

• Remove bin/ scripts in favor of native Nextflow and Python packaging

  formbio/laava#49 · Filter by author etal opened on Jul 12, 2024 · Next
  1

• Use pathlib for file/folder paths

  good first issue
  formbio/laava#48 · Filter by author etal opened on Jul 11, 2024 · Planned

• Use position-sorted BAM instead of name-sorted SAM after initial scan

  formbio/laava#46 · Filter by author etal opened on Jul 9, 2024

• Implement subtype “reverse-packaging” for ITR-only vector+backbone

  formbio/laava#42 · Filter by author etal opened on Jun 24, 2024 · Next

• Accept Sequence and Annotation as Genbank

  enhancement
  formbio/laava#26 · Filter by author bcantarel opened on Jun 1, 2024

• Python type annotations and static type checking

  good first issue
  formbio/laava#21 · Filter by author etal opened on May 23, 2024 · Planned

• Consolidate BED, FASTA file input validation

  formbio/laava#20 · Filter by author etal opened on May 23, 2024 · Planned

• Enable/disable PDF and HTML report formats independently

  enhancement
  formbio/laava#16 · Filter by author etal opened on May 22, 2024 · Planned
  

• Feature request: more annotation in final report

  enhancement
  formbio/laava#12 · Filter by author krobison13 opened on May 13, 2024 · Planned
  2