Issues

• Expand test coverage: stub blocks and corruption edge cases

  area: infraenhancementpriority: medium
  nf-core/fastqrepair#49 · Filter by author mazzalab opened on Aug 22, 2026

• Register a Zenodo DOI and populate manifest.doi

  area: infradocumentationpriority: low
  nf-core/fastqrepair#48 · Filter by author mazzalab opened on Aug 22, 2026

• Migrate publishDir closures to the workflow output block

  area: infraenhancementpriority: low
  nf-core/fastqrepair#47 · Filter by author mazzalab opened on Aug 22, 2026

• Evaluate seqkit sana as an alternative wipe backend

  area: repair-logicenhancementpriority: low
  nf-core/fastqrepair#45 · Filter by author mazzalab opened on Aug 22, 2026

• Auto-detect FASTQ quality encoding instead of assuming Phred+33

  area: repair-logicenhancementpriority: low
  nf-core/fastqrepair#44 · Filter by author mazzalab opened on Aug 22, 2026

• Emit integrity manifest and verify input checksums

  area: ioenhancementpriority: medium
  nf-core/fastqrepair#43 · Filter by author mazzalab opened on Aug 22, 2026

• Add output compression options (bgzf, zstd)

  area: ioenhancementpriority: low
  nf-core/fastqrepair#42 · Filter by author mazzalab opened on Aug 22, 2026

• Support interleaved FASTQ input and output

  area: platform-supportenhancementpriority: medium
  nf-core/fastqrepair#41 · Filter by author mazzalab opened on Aug 22, 2026

• Support long-read (ONT/PacBio) FASTQ

  area: platform-supportenhancementpriority: medium
  nf-core/fastqrepair#40 · Filter by author mazzalab opened on Aug 22, 2026

• Add --validate_only diagnostic mode

  area: repair-logicenhancementpriority: medium
  nf-core/fastqrepair#39 · Filter by author mazzalab opened on Aug 22, 2026

• Housekeeping: remove debug println and stray null file

  area: infrabuggood first issuepriority: low
  nf-core/fastqrepair#37 · Filter by author mazzalab opened on Aug 22, 2026
  1

• Scale num_splits adaptively with input file size

  area: performanceenhancementpriority: medium
  nf-core/fastqrepair#35 · Filter by author mazzalab opened on Aug 22, 2026

• Add optional pre-repair FastQC for before/after comparison

  area: multiqcenhancementpriority: high
  nf-core/fastqrepair#34 · Filter by author mazzalab opened on Aug 22, 2026

• Surface wiper repair reports in MultiQC

  area: multiqcenhancementpriority: high
  nf-core/fastqrepair#33 · Filter by author mazzalab opened on Aug 22, 2026