Issues

• Validate unsupported library strategies before analysis routing

  nf-core/pathogenepidemiology#58 · Filter by author vmduarut opened on Oct 26, 2026

• Reconfigure task memory and cpus to let process labels handle them

  bug
  Task

  nf-core/pathogenepidemiology#52 · Filter by author BilalsGituation opened on Oct 20, 2026
  11

  

• Phylogeny consensus does not select the per-sample BCF genotype

  bug
  nf-core/pathogenepidemiology#50 · Filter by author vmduarut opened on Oct 19, 2026
  2

  

• Discussion: evaluate fastp and Deacon for preprocessing efficiency

  enhancement
  nf-core/pathogenepidemiology#48 · Filter by author vmduarut opened on Oct 19, 2026
  1

• Improve samplesheet ingestion, validation, and pipeline input channels

  enhancement
  nf-core/pathogenepidemiology#47 · Filter by author vmduarut opened on Oct 19, 2026

• Audit whether PICARD_SORTSAM is redundant in GATK_MOI

  enhancement
  nf-core/pathogenepidemiology#46 · Filter by author vmduarut opened on Oct 19, 2026
  5

• Make reference assets reusable through explicit inputs

  enhancement
  nf-core/pathogenepidemiology#45 · Filter by author vmduarut opened on Oct 19, 2026
  

• Migrate publishDir rules to workflow outputs

  enhancement
  nf-core/pathogenepidemiology#44 · Filter by author vmduarut opened on Oct 19, 2026

• PR runs <pipeline> -profile test on file that is gitignored

  bug
  Task

  nf-core/pathogenepidemiology#43 · Filter by author BilalsGituation opened on Oct 17, 2026
  1

• Migrate this work from base functionality to -profile plasmodium

  enhancement
  Task

  nf-core/pathogenepidemiology#28 · Filter by author BilalsGituation opened on Sep 28, 2026

• New module hmmibd-rs

  enhancementhelp wanted
  Task

  nf-core/pathogenepidemiology#27 · Filter by author BilalsGituation opened on Sep 26, 2026
  2

  

• Treatment of Amplicon vs WGS/Genomic samples (decide)

  enhancement
  nf-core/pathogenepidemiology#26 · Filter by author BilalsGituation opened on Sep 26, 2026
  1

• TEST THREAD: tests for upcoming pre-releases

  enhancementhelp wanted
  Enhancement

  nf-core/pathogenepidemiology#25 · Filter by author BilalsGituation opened on Sep 24, 2026
  6

  

• BBDUK step takes forever to test - solutions?

  question
  nf-core/pathogenepidemiology#13 · Filter by author BilalsGituation opened on Aug 3, 2026
  5

  

• Decide details of population-aware layer

  Task

  nf-core/pathogenepidemiology#10 · Filter by author BilalsGituation opened on Jul 29, 2026

• Create short read analysis track

  Task

  nf-core/pathogenepidemiology#7 · Filter by author BilalsGituation opened on Jul 28, 2026
  2

• Handle reference downloads

  Task

  nf-core/pathogenepidemiology#6 · Filter by author BilalsGituation opened on Jul 28, 2026
  1

  

• Integrate code from workflows/original_local.nf into workflows/pathogenepidemiology.nf

  Task

  nf-core/pathogenepidemiology#5 · Filter by author BilalsGituation opened on Jul 28, 2026
  3

  

• Decide on Long Read variant caller that supports polyploidy (fit for MOI analysis)

  Task

  nf-core/pathogenepidemiology#4 · Filter by author BilalsGituation opened on Jul 28, 2026

• Update metromap

  Task

  nf-core/pathogenepidemiology#2 · Filter by author BilalsGituation opened on Jul 28, 2026
  

• Support for samples with long and short read types

  Task

  nf-core/pathogenepidemiology#1 · Filter by author BilalsGituation opened on Jul 28, 2026
  2